diff --git a/src/intersectFile/intersectFile.cpp b/src/intersectFile/intersectFile.cpp
index 32643ac9fc851a20c5ef92b625ae4e31067976e4..87b998d7e66ece23bccef488f368ecba55be65d2 100644
--- a/src/intersectFile/intersectFile.cpp
+++ b/src/intersectFile/intersectFile.cpp
@@ -37,7 +37,7 @@ FileIntersect::~FileIntersect(void) {
delete _recordOutputMgr;
}
-void FileIntersect::processHits(RecordKeyList &hits) {
+void FileIntersect::processHits(RecordKeyVector &hits) {
_recordOutputMgr->printRecord(hits);
}
@@ -58,11 +58,11 @@ bool FileIntersect::processSortedFiles()
return false;
}
- RecordKeyList hitSet;
+ RecordKeyVector hitSet;
while (sweep.next(hitSet)) {
if (_context->getObeySplits()) {
- RecordKeyList keySet(hitSet.getKey());
- RecordKeyList resultSet(hitSet.getKey());
+ RecordKeyVector keySet(hitSet.getKey());
+ RecordKeyVector resultSet(hitSet.getKey());
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
processHits(resultSet);
} else {
@@ -85,11 +85,11 @@ bool FileIntersect::processUnsortedFiles()
if (queryRecord == NULL) {
continue;
}
- RecordKeyList hitSet(queryRecord);
+ RecordKeyVector hitSet(queryRecord);
binTree->getHits(queryRecord, hitSet);
if (_context->getObeySplits()) {
- RecordKeyList keySet(hitSet.getKey());
- RecordKeyList resultSet;
+ RecordKeyVector keySet(hitSet.getKey());
+ RecordKeyVector resultSet;
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
processHits(resultSet);
} else {
diff --git a/src/intersectFile/intersectFile.h b/src/intersectFile/intersectFile.h
index 869e7e159160476eb65f4e7c52431f7cca90f174..585de04427b49cd75f3b620e445f0dbb54c7ac7b 100644
--- a/src/intersectFile/intersectFile.h
+++ b/src/intersectFile/intersectFile.h
@@ -35,7 +35,7 @@ private:
BlockMgr *_blockMgr;
RecordOutputMgr *_recordOutputMgr;
- void processHits(RecordKeyList &hits);
+ void processHits(RecordKeyVector &hits);
bool processSortedFiles();
bool processUnsortedFiles();
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
index 98f140fe4e9f2b6c20d77c4f8cb3a481128131e8..fe33bf9a4ab90cacf3cdc7dede6374f19d3edf52 100644
--- a/src/intersectFile/intersectMain.cpp
+++ b/src/intersectFile/intersectMain.cpp
@@ -12,6 +12,7 @@
#include "intersectFile.h"
#include "ContextIntersect.h"
+#include "CommonHelp.h"
using namespace std;
@@ -47,6 +48,9 @@ void intersect_help(void) {
cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
+ cerr << "\t\t" << "Note: -b may be followed with multiple databases and/or " << endl;
+ cerr << "\t\t" "wildcard (*) character(s). " << endl;
+
cerr << "Options: " << endl;
cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well." << endl << endl;
@@ -120,6 +124,17 @@ void intersect_help(void) {
cerr <<"\t\tother software tools and scripts that need to process one" << endl;
cerr <<"\t\tline of bedtools output at a time." << endl << endl;
+ cerr << "\t-names\t" << "When using multiple databases, provide an alias for each that" << endl;
+ cerr <<"\t\twill appear instead of a fileId when also printing the DB record." << endl << endl;
+
+ cerr << "\t-filenames" << "\tWhen using multiple databases, show each complete filename" << endl;
+ cerr <<"\t\t\tinstead of a fileId when also printing the DB record." << endl << endl;
+
+ cerr << "\t-sortout\t" << "When using multiple databases, sort the output DB hits" << endl;
+ cerr << "\t\t\tfor each record." << endl << endl;
+
+ CommonHelp();
+
cerr << "Notes: " << endl;
cerr << "\t(1) When a BAM file is used for the A file, the alignment is retained if overlaps exist," << endl;
cerr << "\tand exlcuded if an overlap cannot be found. If multiple overlaps exist, they are not" << endl;
diff --git a/src/jaccard/Jaccard.cpp b/src/jaccard/Jaccard.cpp
index cf3d7136d393d154f72b86a0062fc9987a0bdb83..3ccda00d34320b5a7b8134641a18d642f8eac069 100644
--- a/src/jaccard/Jaccard.cpp
+++ b/src/jaccard/Jaccard.cpp
@@ -49,11 +49,11 @@ bool Jaccard::getIntersectionAndUnion() {
if (!sweep.init()) {
return false;
}
- RecordKeyList hitSet;
+ RecordKeyVector hitSet;
while (sweep.next(hitSet)) {
if (_context->getObeySplits()) {
- RecordKeyList keySet(hitSet.getKey());
- RecordKeyList resultSet(hitSet.getKey());
+ RecordKeyVector keySet(hitSet.getKey());
+ RecordKeyVector resultSet(hitSet.getKey());
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
_intersectionVal += getTotalIntersection(&resultSet);
} else {
@@ -69,7 +69,7 @@ bool Jaccard::getIntersectionAndUnion() {
return true;
}
-unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
+unsigned long Jaccard::getTotalIntersection(RecordKeyVector *recList)
{
unsigned long intersection = 0;
const Record *key = recList->getKey();
@@ -77,8 +77,8 @@ unsigned long Jaccard::getTotalIntersection(RecordKeyList *recList)
int keyEnd = key->getEndPos();
int hitIdx = 0;
- for (RecordKeyList::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
- const Record *currRec = iter->value();
+ for (RecordKeyVector::const_iterator_type iter = recList->begin(); iter != recList->end(); iter = recList->next()) {
+ const Record *currRec = *iter;
int maxStart = max(currRec->getStartPos(), keyStart);
int minEnd = min(currRec->getEndPos(), keyEnd);
if (_context->getObeySplits()) {
diff --git a/src/jaccard/Jaccard.h b/src/jaccard/Jaccard.h
index 21a90f6fb94d9108e41a71c08b7572d18ff8a915..3d61e8f8c00fa5121cfebff4d10b519ce75bcad4 100644
--- a/src/jaccard/Jaccard.h
+++ b/src/jaccard/Jaccard.h
@@ -33,7 +33,7 @@ private:
int _numIntersections;
bool getIntersectionAndUnion();
- unsigned long getTotalIntersection(RecordKeyList *hits);
+ unsigned long getTotalIntersection(RecordKeyVector *hits);
};
#endif /* JACCARD_H */
diff --git a/src/mapFile/mapFile.cpp b/src/mapFile/mapFile.cpp
index 8dbf24ad54a2e93715fd453092e778efcdf24b0c..e78b59c0b6a9ccd1c5bef5efe6321bcb824b841c 100644
--- a/src/mapFile/mapFile.cpp
+++ b/src/mapFile/mapFile.cpp
@@ -41,11 +41,11 @@ bool FileMap::mapFiles()
if (!sweep.init()) {
return false;
}
- RecordKeyList hitSet;
+ RecordKeyVector hitSet;
while (sweep.next(hitSet)) {
if (_context->getObeySplits()) {
- RecordKeyList keySet(hitSet.getKey());
- RecordKeyList resultSet(hitSet.getKey());
+ RecordKeyVector keySet(hitSet.getKey());
+ RecordKeyVector resultSet(hitSet.getKey());
_blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
_recordOutputMgr->printRecord(resultSet.getKey(), _context->getColumnOpsVal(resultSet));
} else {
diff --git a/src/mapFile/mapFile.h b/src/mapFile/mapFile.h
index 38cbcda1f1b1e78cb0bde8cb2c0ab00b37c3e0e2..df92220235302d7a5dbd534a98fb10af058a943c 100644
--- a/src/mapFile/mapFile.h
+++ b/src/mapFile/mapFile.h
@@ -15,7 +15,7 @@
#include <sstream>
#include <iomanip>
#include "VectorOps.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
#include "ContextMap.h"
using namespace std;
diff --git a/src/mergeFile/mergeFile.cpp b/src/mergeFile/mergeFile.cpp
index f772629c440db0fae1ab9e7535491fc6d2edf4eb..e4a3c863c579fd78eeaf8d3946cb5aeeef96fdac 100644
--- a/src/mergeFile/mergeFile.cpp
+++ b/src/mergeFile/mergeFile.cpp
@@ -28,7 +28,7 @@ MergeFile::~MergeFile()
bool MergeFile::merge()
{
- RecordKeyList hitSet;
+ RecordKeyVector hitSet;
FileRecordMgr *frm = _context->getFile(0);
while (!frm->eof()) {
Record *key = frm->getNextRecord(&hitSet);
diff --git a/src/utils/BinTree/BinTree.cpp b/src/utils/BinTree/BinTree.cpp
index 253dea2798320bfd7886931213612b2c21931baf..5dce775b06c9facfb02d54d757e74d43d76fb909 100644
--- a/src/utils/BinTree/BinTree.cpp
+++ b/src/utils/BinTree/BinTree.cpp
@@ -3,8 +3,7 @@
BinTree::BinTree(ContextIntersect *context)
-: _databaseFile(NULL),
- _context(context),
+: _context(context),
_binOffsetsExtended(NULL),
_showBinMetrics(false),
_maxBinNumFound(0)
@@ -36,7 +35,7 @@ BinTree::~BinTree() {
}
for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
const Record *record = listIter->value();
- _databaseFile->deleteRecord(record);
+ _context->getFile(record->getFileIdx())->deleteRecord(record);
}
delete bin;
bin = NULL;
@@ -70,25 +69,27 @@ BinTree::~BinTree() {
void BinTree::loadDB()
{
- _databaseFile = _context->getFile(_context->getDatabaseFileIdx());
-
- Record *record = NULL;
- while (!_databaseFile->eof()) {
- record = _databaseFile->getNextRecord();
- //In addition to NULL records, we also don't want to add unmapped reads.
- if (record == NULL || record->isUnmapped()) {
- continue;
- }
+ for (int i=0; i < _context->getNumDatabaseFiles(); i++) {
+ FileRecordMgr *databaseFile = _context->getDatabaseFile(i);
+
+ Record *record = NULL;
+ while (!databaseFile->eof()) {
+ record = databaseFile->getNextRecord();
+ //In addition to NULL records, we also don't want to add unmapped reads.
+ if (record == NULL || record->isUnmapped()) {
+ continue;
+ }
- if (!addRecordToTree(record)) {
- fprintf(stderr, "ERROR: Unable to add record to tree.\n");
- _databaseFile->close();
- exit(1);
+ if (!addRecordToTree(record)) {
+ fprintf(stderr, "ERROR: Unable to add record to tree.\n");
+ databaseFile->close();
+ exit(1);
+ }
}
}
}
-void BinTree::getHits(Record *record, RecordKeyList &hitSet)
+void BinTree::getHits(Record *record, RecordKeyVector &hitSet)
{
if (_showBinMetrics) {
return; //don't care about query entries just yet.
@@ -149,6 +150,9 @@ void BinTree::getHits(Record *record, RecordKeyList &hitSet)
startBin >>= _binNextShift;
endBin >>= _binNextShift;
}
+ if (_context->getSortOutput()) {
+ hitSet.sortVector();
+ }
}
bool BinTree::addRecordToTree(const Record *record)
diff --git a/src/utils/BinTree/BinTree.h b/src/utils/BinTree/BinTree.h
index 161696c1739763530f21a500a161cea0ef06aad1..cd981c293e18c75b4276593d1795b72c5e3d49a3 100644
--- a/src/utils/BinTree/BinTree.h
+++ b/src/utils/BinTree/BinTree.h
@@ -28,11 +28,10 @@ public:
~BinTree();
void loadDB();
- void getHits(Record *record, RecordKeyList &hitSet);
+ void getHits(Record *record, RecordKeyVector &hitSet);
private:
- FileRecordMgr *_databaseFile;
ContextIntersect *_context;
//
@@ -52,8 +51,8 @@ private:
static const uint32_t _binFirstShift = 14; /* How much to shift to get to finest bin. */
static const uint32_t _binNextShift = 3; /* How much to shift to get to next larger bin. */
- typedef BTlist<const Record *> innerListType;
- typedef const BTlistNode<const Record *> * innerListIterType;
+ typedef RecordList innerListType;
+ typedef const RecordListNode * innerListIterType;
typedef innerListType * binType;
typedef binType * allBinsType;
typedef QuickString mainKeyType;
diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
index 60fbd9330585d673b26ff596a22b3d5fd707f421..6fa01c1b5fc0bf241404afe422da0ef0ec219109 100644
--- a/src/utils/Contexts/ContextBase.cpp
+++ b/src/utils/Contexts/ContextBase.cpp
@@ -36,18 +36,17 @@ ContextBase::ContextBase()
_reciprocal(false),
_sameStrand(false),
_diffStrand(false),
- _sortedInput(false),
+ _sortedInput(false),
+ _sortOutput(false),
+ _reportDBnameTags(false),
+ _reportDBfileNames(false),
_printHeader(false),
_printable(true),
_explicitBedOutput(false),
_queryFileIdx(-1),
- _databaseFileIdx(-1),
_bamHeaderAndRefIdx(-1),
_maxNumDatabaseFields(0),
_useFullBamTags(false),
- _reportCount(false),
- _reportNames(false),
- _reportScores(false),
_numOutputRecords(0),
_hasConstantSeed(false),
_seed(0),
@@ -193,6 +192,9 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
else if (strcmp(_argv[_i], "-delim") == 0) {
if (!handle_delim()) return false;
}
+ else if (strcmp(_argv[_i], "-sortout") == 0) {
+ if (!handle_sortout()) return false;
+ }
}
return true;
@@ -210,7 +212,11 @@ bool ContextBase::isValidState()
return false;
}
if (hasColumnOpsMethods()) {
- FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+
+ //TBD: Adjust column ops for multiple databases.
+ //For now, use last file.
+// FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+ FileRecordMgr *dbFile = getFile(getNumInputFiles()-1);
_keyListOps->setDBfileType(dbFile->getFileType());
if (!_keyListOps->isValidColumnOps(dbFile)) {
return false;
@@ -251,7 +257,7 @@ bool ContextBase::openFiles() {
_files.resize(_fileNames.size());
for (int i = 0; i < (int)_fileNames.size(); i++) {
- FileRecordMgr *frm = getNewFRM(_fileNames[i]);
+ FileRecordMgr *frm = getNewFRM(_fileNames[i], i);
if (hasGenomeFile()) {
frm->setGenomeFile(_genomeFile);
}
@@ -281,7 +287,7 @@ int ContextBase::getBamHeaderAndRefIdx() {
if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_bamHeaderAndRefIdx = _queryFileIdx;
} else {
- _bamHeaderAndRefIdx = _databaseFileIdx;
+ _bamHeaderAndRefIdx = _dbFileIdxs[0];
}
return _bamHeaderAndRefIdx;
}
@@ -492,6 +498,13 @@ bool ContextBase::handle_delim()
return true;
}
+bool ContextBase::handle_sortout()
+{
+ setSortOutput(true);
+ markUsed(_i - _skipFirstArgs);
+ return true;
+}
+
void ContextBase::setColumnOpsMethods(bool val)
{
if (val && !_hasColumnOpsMethods) {
@@ -501,20 +514,24 @@ void ContextBase::setColumnOpsMethods(bool val)
_hasColumnOpsMethods = val;
}
-const QuickString &ContextBase::getColumnOpsVal(RecordKeyList &keyList) const {
+const QuickString &ContextBase::getColumnOpsVal(RecordKeyVector &keyList) const {
if (!hasColumnOpsMethods()) {
return _nullStr;
}
return _keyListOps->getOpVals(keyList);
}
-FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename) {
- if (!_useMergedIntervals) {
- return new FileRecordMgr(filename);
- } else {
+FileRecordMgr *ContextBase::getNewFRM(const QuickString &filename, int fileIdx) {
+
+ if (_useMergedIntervals) {
FileRecordMergeMgr *frm = new FileRecordMergeMgr(filename);
frm->setStrandType(_desiredStrand);
frm->setMaxDistance(_maxDistance);
+ frm->setFileIdx(fileIdx);
+ return frm;
+ } else {
+ FileRecordMgr *frm = new FileRecordMgr(filename);
+ frm->setFileIdx(fileIdx);
return frm;
}
}
diff --git a/src/utils/Contexts/ContextBase.h b/src/utils/Contexts/ContextBase.h
index d28b9e6ade6e4e5fcd5cd3591962ffd3c52eab6a..1c6cecbdbe66ab8dafcb11875bf0a9835b2ba331 100644
--- a/src/utils/Contexts/ContextBase.h
+++ b/src/utils/Contexts/ContextBase.h
@@ -98,6 +98,15 @@ public:
virtual bool getSortedInput() const {return _sortedInput; }
virtual void setSortedInput(bool val) { _sortedInput = val; }
+ virtual bool getSortOutput() const {return _sortOutput; }
+ virtual void setSortOutput(bool val) { _sortOutput = val; }
+
+ virtual bool getUseDBnameTags() const { return _reportDBnameTags; }
+ virtual void setUseDBnameTags(bool val) { _reportDBnameTags = val; }
+
+ virtual bool getUseDBfileNames() const { return _reportDBfileNames; }
+ virtual void setUseDBfileNames(bool val) { _reportDBfileNames = val; }
+
virtual bool getPrintHeader() const {return _printHeader; }
virtual void setPrintHeader(bool val) { _printHeader = val; }
@@ -107,24 +116,6 @@ public:
virtual bool getUseFullBamTags() const { return _useFullBamTags; }
virtual void setUseFullBamTags(bool val) { _useFullBamTags = val; }
-// //
-// // MERGE METHODS
-// //
-// virtual bool getReportCount() const { return _reportCount; }
-// virtual void setReportCount(bool val) { _reportCount = val; }
-//
-// virtual int getMaxDistance() const { return _maxDistance; }
-// virtual void setMaxDistance(int distance) { _maxDistance = distance; }
-//
-// virtual bool getReportNames() const { return _reportNames; }
-// virtual void setReportNames(bool val) { _reportNames = val; }
-//
-// virtual bool getReportScores() const { return _reportScores; }
-// virtual void setReportScores(bool val) { _reportScores = val; }
-//
-// virtual const QuickString &getScoreOp() const { return _scoreOp; }
-// virtual void setScoreOp(const QuickString &op) { _scoreOp = op; }
-
// METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER
// OF OUTPUT RECORDS.
@@ -150,7 +141,7 @@ public:
// are available.
void setColumnOpsMethods(bool val);
virtual bool hasColumnOpsMethods() const { return _hasColumnOpsMethods; }
- const QuickString &getColumnOpsVal(RecordKeyList &keyList) const;
+ const QuickString &getColumnOpsVal(RecordKeyVector &keyList) const;
//methods applicable only to column operations.
protected:
@@ -192,18 +183,19 @@ protected:
bool _sameStrand;
bool _diffStrand;
bool _sortedInput;
+ bool _sortOutput;
+ bool _reportDBnameTags;
+ bool _reportDBfileNames;
bool _printHeader;
bool _printable;
bool _explicitBedOutput;
int _queryFileIdx;
- int _databaseFileIdx;
+ vector<int> _dbFileIdxs;
+ vector<QuickString> _dbNameTags;
+ map<int, int> _fileIdsToDbIdxs;
int _bamHeaderAndRefIdx;
int _maxNumDatabaseFields;
bool _useFullBamTags;
- bool _reportCount;
- bool _reportNames;
- bool _reportScores;
- QuickString _scoreOp;
int _numOutputRecords;
@@ -227,7 +219,7 @@ protected:
bool isUsed(int i) const { return _argsProcessed[i]; }
bool cmdArgsValid();
bool openFiles();
- virtual FileRecordMgr *getNewFRM(const QuickString &filename);
+ virtual FileRecordMgr *getNewFRM(const QuickString &filename, int fileIdx);
//set cmd line params and counter, i, as members so code
//is more readable (as opposed to passing all 3 everywhere).
@@ -256,6 +248,7 @@ protected:
virtual bool handle_o();
virtual bool handle_null();
virtual bool handle_delim();
+ virtual bool handle_sortout();
bool parseIoBufSize(QuickString bufStr);
diff --git a/src/utils/Contexts/ContextIntersect.cpp b/src/utils/Contexts/ContextIntersect.cpp
index fecf51d115ebde0c87446c9341cb95e1cf4b89ea..1ef4b3d312f4fc6323a1595306828c6fd1eda9f6 100644
--- a/src/utils/Contexts/ContextIntersect.cpp
+++ b/src/utils/Contexts/ContextIntersect.cpp
@@ -44,6 +44,12 @@ bool ContextIntersect::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
else if (strcmp(_argv[_i], "-b") == 0) {
if (!handle_b()) return false;
}
+ else if (strcmp(_argv[_i], "-names") == 0) {
+ if (!handle_names()) return false;
+ }
+ else if (strcmp(_argv[_i], "-filenames") == 0) {
+ if (!handle_filenames()) return false;
+ }
else if (strcmp(_argv[_i], "-u") == 0) {
if (!handle_u()) return false;
}
@@ -92,7 +98,7 @@ bool ContextIntersect::isValidState()
return false;
}
- if (_queryFileIdx == -1 || _databaseFileIdx == -1) {
+ if (_queryFileIdx == -1 || _dbFileIdxs.size() == -0) {
_errorMsg = "\n***** ERROR: query and database files not specified. *****";
return false;
}
@@ -113,6 +119,11 @@ bool ContextIntersect::isValidState()
return false;
}
}
+ if (getUseDBnameTags() && _dbNameTags.size() != _dbFileIdxs.size()) {
+ _errorMsg = "\n***** ERROR: Number of database name tags given does not match number of databases. *****";
+ return false;
+
+ }
if (getWriteOverlap()) {
if (getWriteA()) {
@@ -149,7 +160,7 @@ bool ContextIntersect::isValidState()
if (getAnyHit() || getNoHit() || getWriteCount()) {
setPrintable(false);
}
- if (_files.size() != 2 ) {
+ if (_files.size() < 2 ) {
return false;
}
return true;
@@ -161,8 +172,8 @@ bool ContextIntersect::determineOutputType() {
}
//determine the maximum number of database fields.
- for (int i=0; i < (int)_files.size(); i++) {
- int numFields = _files[i]->getNumFields();
+ for (int i=0; i < getNumDatabaseFiles(); i++) {
+ int numFields = getDatabaseFile(i)->getNumFields();
if ( numFields > _maxNumDatabaseFields) {
_maxNumDatabaseFields = numFields;
}
@@ -211,19 +222,46 @@ bool ContextIntersect::handle_abam()
bool ContextIntersect::handle_b()
{
if (_argc <= _i+1) {
- _errorMsg = "\n***** ERROR: -b option given, but no query file specified. *****";
+ _errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
return false;
}
- addInputFile(_argv[_i+1]);
- _databaseFileIdx = getNumInputFiles() -1;
- markUsed(_i - _skipFirstArgs);
- _i++;
- markUsed(_i - _skipFirstArgs);
+ do {
+ addInputFile(_argv[_i+1]);
+ int fileId = getNumInputFiles() -1;
+ _dbFileIdxs.push_back(fileId);
+ _fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ } while (_argc > _i+1 && _argv[_i+1][0] != '-');
return true;
}
+bool ContextIntersect::handle_names()
+{
+ if (_argc <= _i+1) {
+ _errorMsg = "\n***** ERROR: -b option given, but no database names specified. *****";
+ return false;
+ }
+
+ do {
+ addDatabaseNameTag(_argv[_i+1]);
+ markUsed(_i - _skipFirstArgs);
+ _i++;
+ markUsed(_i - _skipFirstArgs);
+ } while (_argc > _i+1 && _argv[_i+1][0] != '-');
+ setUseDBnameTags(true);
+ return true;
+}
+
+bool ContextIntersect::handle_filenames()
+{
+ markUsed(_i - _skipFirstArgs);
+ setUseDBfileNames(true);
+ return true;
+}
bool ContextIntersect::handle_c()
{
diff --git a/src/utils/Contexts/ContextIntersect.h b/src/utils/Contexts/ContextIntersect.h
index b066e9465eac744b8bed21dcd3c39c935407345c..9bb20464124bbae9e2d7d076158bff5921ac9fd9 100644
--- a/src/utils/Contexts/ContextIntersect.h
+++ b/src/utils/Contexts/ContextIntersect.h
@@ -22,19 +22,22 @@ public:
//NOTE: Query and database files will only be marked as such by either the
//parseCmdArgs method, or by explicitly setting them.
FileRecordMgr *getQueryFile() { return getFile(_queryFileIdx); }
- FileRecordMgr *getDatabaseFile() { return getFile(_databaseFileIdx); }
+ FileRecordMgr *getDatabaseFile(int idx) { return getFile(_dbFileIdxs[idx]); }
int getQueryFileIdx() const { return _queryFileIdx; }
void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
- int getDatabaseFileIdx() const { return _databaseFileIdx; }
- void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
+ int getNumDatabaseFiles() { return (int)_dbFileIdxs.size(); }
+ const vector<int> &getDbFileIdxs() const { return _dbFileIdxs; }
const QuickString &getQueryFileName() const { return _files[_queryFileIdx]->getFileName(); }
- const QuickString &getDatabaseFileName() const { return _files[_databaseFileIdx]->getFileName(); }
+ const QuickString &getDatabaseFileName(int idx) const { return _files[_dbFileIdxs[idx]]->getFileName(); }
ContextFileType getQueryFileType() const { return _files[_queryFileIdx]->getFileType(); }
- ContextFileType getDatabaseFileType() const { return _files[_databaseFileIdx]->getFileType(); }
+ ContextFileType getDatabaseFileType(int idx) const { return _files[_dbFileIdxs[idx]]->getFileType(); }
ContextRecordType getQueryRecordType() const { return _files[_queryFileIdx]->getRecordType(); }
- ContextRecordType getDatabaseRecordType() const { return _files[_databaseFileIdx]->getRecordType(); }
+ ContextRecordType getDatabaseRecordType(int idx) const { return _files[_dbFileIdxs[idx]]->getRecordType(); }
int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
+ int getDbIdx(int fileId) { return _fileIdsToDbIdxs.find(fileId)->second; }
+ void addDatabaseNameTag(const QuickString &tag) { _dbNameTags.push_back(tag); }
+ const QuickString &getDatabaseNameTag(int dbIdx) const { return _dbNameTags[dbIdx]; }
bool getAnyHit() const {return _anyHit; }
void setAnyHit(bool val) { _anyHit = val; }
@@ -83,6 +86,9 @@ private:
virtual bool handle_a();
virtual bool handle_abam();
virtual bool handle_b();
+ virtual bool handle_names();
+ virtual bool handle_filenames();
+
virtual bool handle_c();
virtual bool handle_f();
virtual bool handle_loj();
diff --git a/src/utils/Contexts/ContextMap.cpp b/src/utils/Contexts/ContextMap.cpp
index e6abc519501a1e5320c5aad4103bd04fc083096a..1d79d7a690d750bbdbe1435e42c05bcacb2a5f24 100644
--- a/src/utils/Contexts/ContextMap.cpp
+++ b/src/utils/Contexts/ContextMap.cpp
@@ -47,3 +47,17 @@ bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
}
return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
}
+
+bool ContextMap::isValidState()
+{
+ if (!ContextIntersect::isValidState()) {
+ return false;
+ }
+
+ // Multiple databases are currently not supported
+ if (getNumDatabaseFiles() > 1) {
+ _errorMsg = "\n***** ERROR: multiple database files currently not supported for map. *****";
+ return false;
+ }
+ return true;
+}
diff --git a/src/utils/Contexts/ContextMap.h b/src/utils/Contexts/ContextMap.h
index fb23f4d5412fedcd3599f3951fd5e24bd76dbfb0..53240af65f9a7e1cce65fab3ed7a13c1aadbefda 100644
--- a/src/utils/Contexts/ContextMap.h
+++ b/src/utils/Contexts/ContextMap.h
@@ -16,6 +16,8 @@ public:
virtual ~ContextMap();
virtual bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
virtual bool hasIntersectMethods() const { return true; }
+ virtual bool isValidState();
+
private:
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.cpp b/src/utils/FileRecordTools/FileReaders/FileReader.cpp
index 967b82a0052c5b1c374efc32b4349e1e84d57768..de495810bf862c8816285643e64824e1662b31b1 100644
--- a/src/utils/FileRecordTools/FileReaders/FileReader.cpp
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.cpp
@@ -4,7 +4,7 @@
#include "BufferedStreamMgr.h"
FileReader::FileReader()
-:
+: _fileIdx(-1),
_bufStreamMgr(NULL),
_isFileOpen(false),
_currChromId(-1)
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.h b/src/utils/FileRecordTools/FileReaders/FileReader.h
index 73a968bace4b39e9b0b5c6536e959834a1cf88d1..48b861ad70876587a89a5927fa4f3edfecb8e6b2 100644
--- a/src/utils/FileRecordTools/FileReaders/FileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.h
@@ -16,6 +16,9 @@ public:
FileReader();
virtual ~FileReader();
void setFileName(const string &filename) { _filename = filename; }
+ virtual int getFileIdx() const { return _fileIdx; }
+ virtual void setFileIdx(int fileIdx) { _fileIdx = fileIdx; }
+
void setInputStream(BufferedStreamMgr *bufStreamMgr) {
_bufStreamMgr = bufStreamMgr;
_isFileOpen = true;
@@ -31,6 +34,7 @@ public:
virtual const QuickString &getHeader() const =0;
virtual int getNumFields() const = 0;
protected:
+ int _fileIdx;
string _filename;
BufferedStreamMgr *_bufStreamMgr;
diff --git a/src/utils/FileRecordTools/FileReaders/Makefile b/src/utils/FileRecordTools/FileReaders/Makefile
index 37ff6e89f0cc87f1b4597dbc2f6fba8a6b9b4a8e..20c9c0ed179eec073da20a253e2fe301bc52e310 100644
--- a/src/utils/FileRecordTools/FileReaders/Makefile
+++ b/src/utils/FileRecordTools/FileReaders/Makefile
@@ -17,10 +17,10 @@ INCLUDES = -I$(UTILITIES_DIR)/BamTools/include/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= FileReader.h FileReader.cpp SingleLineDelimTransferBuffer.h SingleLineDelimTransferBuffer.cpp \
+SOURCES= FileReader.h FileReader.cpp \
SingleLineDelimTextFileReader.h SingleLineDelimTextFileReader.cpp BamFileReader.h BamFileReader.cpp \
BufferedStreamMgr.h BufferedStreamMgr.cpp InputStreamMgr.h InputStreamMgr.cpp
-OBJECTS= FileReader.o SingleLineDelimTransferBuffer.o SingleLineDelimTextFileReader.o BamFileReader.o BufferedStreamMgr.o InputStreamMgr.o
+OBJECTS= FileReader.o SingleLineDelimTextFileReader.o BamFileReader.o BufferedStreamMgr.o InputStreamMgr.o
_EXT_OBJECTS=ParseTools.o QuickString.o CompressionTools.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -35,7 +35,7 @@ $(BUILT_OBJECTS): $(SOURCES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/FileReader.o $(OBJ_DIR)SingleLineDelimTransferBuffer $(OBJ_DIR)/SingleLineDelimTextFileReader.o \
+ @rm -f $(OBJ_DIR)/FileReader.o $(OBJ_DIR)/SingleLineDelimTextFileReader.o \
$(OBJ_DIR)/BinaryFileReader.o $(OBJ_DIR)/BamFileReader.o $(OBJ_DIR)/BufferedStreamMgr.o $(OBJ_DIR)/InputStreamMgr.o $(OBJ_DIR)/PushBackGzStream.o
.PHONY: clean
diff --git a/src/utils/FileRecordTools/FileReaders/Makefile~ b/src/utils/FileRecordTools/FileReaders/Makefile~
new file mode 100644
index 0000000000000000000000000000000000000000..37ff6e89f0cc87f1b4597dbc2f6fba8a6b9b4a8e
--- /dev/null
+++ b/src/utils/FileRecordTools/FileReaders/Makefile~
@@ -0,0 +1,41 @@
+OBJ_DIR = ../../../../obj/
+BIN_DIR = ../../../../bin/
+UTILITIES_DIR = ../../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/BamTools/include/ \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/gzstream/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= FileReader.h FileReader.cpp SingleLineDelimTransferBuffer.h SingleLineDelimTransferBuffer.cpp \
+ SingleLineDelimTextFileReader.h SingleLineDelimTextFileReader.cpp BamFileReader.h BamFileReader.cpp \
+ BufferedStreamMgr.h BufferedStreamMgr.cpp InputStreamMgr.h InputStreamMgr.cpp
+OBJECTS= FileReader.o SingleLineDelimTransferBuffer.o SingleLineDelimTextFileReader.o BamFileReader.o BufferedStreamMgr.o InputStreamMgr.o
+_EXT_OBJECTS=ParseTools.o QuickString.o CompressionTools.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+all: $(BUILT_OBJECTS)
+
+.PHONY: all
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/FileReader.o $(OBJ_DIR)SingleLineDelimTransferBuffer $(OBJ_DIR)/SingleLineDelimTextFileReader.o \
+ $(OBJ_DIR)/BinaryFileReader.o $(OBJ_DIR)/BamFileReader.o $(OBJ_DIR)/BufferedStreamMgr.o $(OBJ_DIR)/InputStreamMgr.o $(OBJ_DIR)/PushBackGzStream.o
+
+.PHONY: clean
diff --git a/src/utils/FileRecordTools/FileRecordMergeMgr.cpp b/src/utils/FileRecordTools/FileRecordMergeMgr.cpp
index 7c7461fa0f4a98458cbb52d79857b50d78c46faa..40e42b3f3352c483c9cf83ec9baffca513bfb971 100644
--- a/src/utils/FileRecordTools/FileRecordMergeMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMergeMgr.cpp
@@ -16,7 +16,7 @@ FileRecordMergeMgr::FileRecordMergeMgr(const QuickString & filename)
}
//Record *FileRecordMergeMgr::allocateAndGetNextMergedRecord(WANT_STRAND_TYPE desiredStrand, int maxDistance) {
-// RecordKeyList recList;
+// RecordKeyVector recList;
// if (!allocateAndGetNextMergedRecord(recList, desiredStrand, maxDistance)) {
// return NULL;
// }
@@ -24,7 +24,7 @@ FileRecordMergeMgr::FileRecordMergeMgr(const QuickString & filename)
// return const_cast<Record *>(recList.getKey()); //want key to be non-const
//}
-Record *FileRecordMergeMgr::getNextRecord(RecordKeyList *recList)
+Record *FileRecordMergeMgr::getNextRecord(RecordKeyVector *recList)
{
//clear the recList if there is one, and if it has records
// in it.
@@ -191,7 +191,7 @@ Record *FileRecordMergeMgr::tryToTakeFromStorage(Record::strandType strand) {
return record;
}
-void FileRecordMergeMgr::deleteMergedRecord(RecordKeyList &recList)
+void FileRecordMergeMgr::deleteMergedRecord(RecordKeyVector &recList)
{
deleteAllMergedItemsButKey(recList);
deleteRecord(recList.getKey());
@@ -203,15 +203,15 @@ bool FileRecordMergeMgr::eof(){
}
-void FileRecordMergeMgr::deleteAllMergedItemsButKey(RecordKeyList &recList) {
+void FileRecordMergeMgr::deleteAllMergedItemsButKey(RecordKeyVector &recList) {
//if the key is also in the list, this method won't delete it.
- for (RecordKeyList::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
- if (iter->value() == recList.getKey()) {
+ for (RecordKeyVector::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
+ if (*iter == recList.getKey()) {
continue;
}
- deleteRecord(iter->value());
+ deleteRecord(*iter);
}
- recList.clearList();
+ recList.clearVector();
}
diff --git a/src/utils/FileRecordTools/FileRecordMergeMgr.h b/src/utils/FileRecordTools/FileRecordMergeMgr.h
index aecdeefd856debcbc29dbf352165b1a78c936f15..ce6cfcfa5bc5a2e865b2c4b1b900563757067cbf 100644
--- a/src/utils/FileRecordTools/FileRecordMergeMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMergeMgr.h
@@ -22,13 +22,13 @@ public:
//
// This will give a single "meta" record containing "flattened" or merged records.
//
- // Pass an empty RecordKeyList. When done, will have a pair: 1st is the final merged record,
+ // Pass an empty RecordKeyVector. When done, will have a pair: 1st is the final merged record,
// second is list of constituent Records merged.
//
///////////////////////////////////////////////////////////////////////////////////
- Record *getNextRecord(RecordKeyList *keyList = NULL);
- void deleteMergedRecord(RecordKeyList &recList); // MUST use this method for cleanup!
+ Record *getNextRecord(RecordKeyVector *keyList = NULL);
+ void deleteMergedRecord(RecordKeyVector &recList); // MUST use this method for cleanup!
bool eof();
@@ -48,7 +48,7 @@ private:
int _maxDistance;
StrandQueue _storedRecords;
- void deleteAllMergedItemsButKey(RecordKeyList &recList);
+ void deleteAllMergedItemsButKey(RecordKeyVector &recList);
void addToStorage(Record *record);
Record *tryToTakeFromStorage();
Record *tryToTakeFromStorage(Record::strandType strand);
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index fc8a986e5dd416344fef8e3b51751aa76136bb81..4386961115812378a65582bc31686383161338e1 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -5,7 +5,7 @@
#include "NewGenomeFile.h"
FileRecordMgr::FileRecordMgr(const QuickString &filename)
-:
+: _fileIdx(-1),
_filename(filename),
_bufStreamMgr(NULL),
_fileReader(NULL),
@@ -90,7 +90,7 @@ bool FileRecordMgr::eof(){
return _fileReader->eof();
}
-Record *FileRecordMgr::getNextRecord(RecordKeyList *keyList)
+Record *FileRecordMgr::getNextRecord(RecordKeyVector *keyList)
{
if (!_fileReader->isOpen()) {
return NULL;
@@ -203,7 +203,7 @@ void FileRecordMgr::deleteRecord(const Record *record) {
_recordMgr->deleteRecord(record);
}
-void FileRecordMgr::deleteRecord(RecordKeyList *keyList) {
+void FileRecordMgr::deleteRecord(RecordKeyVector *keyList) {
_recordMgr->deleteRecord(keyList->getKey());
}
@@ -224,6 +224,7 @@ void FileRecordMgr::allocateFileReader()
default:
break;
}
+ _fileReader->setFileIdx(_fileIdx);
}
const BamTools::RefVector & FileRecordMgr::getBamReferences() {
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
index 95e459e7add14b299fc45e6043d71f89aeb1d2db..ac3bc1289d98ff403d328c6148fdf21b9cbe9273 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -22,7 +22,7 @@
//record manager and all record classes
#include "RecordMgr.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
#include "BlockMgr.h"
using namespace std;
@@ -37,14 +37,19 @@ public:
bool open();
void close();
virtual bool eof();
+ void setFileIdx(int fileIdx) { _fileIdx = fileIdx; }
+ int getFileIdx() const { return _fileIdx; }
+
//This is an all-in-one method to give the user a new record that is initialized with
//the next entry in the data file.
//NOTE!! User MUST pass back the returned pointer to deleteRecord method for cleanup!
//Also Note! User must check for NULL returned, meaning we failed to get the next record.
- virtual Record *getNextRecord(RecordKeyList *keyList = NULL);
+ virtual Record *getNextRecord(RecordKeyVector *keyList = NULL);
void deleteRecord(const Record *);
- virtual void deleteRecord(RecordKeyList *keyList);
+ virtual void deleteRecord(RecordKeyVector *keyList);
+
+
const QuickString &getFileName() const { return _filename;}
bool hasHeader() const { return _fileReader->hasHeader(); }
@@ -103,6 +108,7 @@ public:
void setIoBufSize(int val) { _ioBufSize = val; }
protected:
+ int _fileIdx;
QuickString _filename;
BufferedStreamMgr *_bufStreamMgr;
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index a55a0615e400d41b2ef3aacd84e78c2b45ae188d..9c3bd5a310e152967f5a364752c2d40d8e84425f 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -7,7 +7,7 @@
#include "BamRecord.h"
#include "BamFileReader.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
BamRecord::BamRecord()
: _bamChromId(-1)
@@ -45,6 +45,7 @@ bool BamRecord::initFromFile(FileReader *fileReader)
bool BamRecord::initFromFile(BamFileReader *bamFileReader)
{
+ setFileIdx(bamFileReader->getFileIdx());
_bamAlignment = bamFileReader->getAlignment();
bamFileReader->getChrName(_chrName);
@@ -116,19 +117,19 @@ void BamRecord::clear()
}
-void BamRecord::print(QuickString &outBuf, RecordKeyList *keyList) const
+void BamRecord::print(QuickString &outBuf, RecordKeyVector *keyList) const
{
Bed6Interval::print(outBuf);
printRemainingBamFields(outBuf, keyList);
}
-void BamRecord::print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const
+void BamRecord::print(QuickString &outBuf, int start, int end, RecordKeyVector *keyList) const
{
Bed6Interval::print(outBuf, start, end);
printRemainingBamFields(outBuf, keyList);
}
-void BamRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const
+void BamRecord::print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyVector *keyList) const
{
Bed6Interval::print(outBuf, start, end);
printRemainingBamFields(outBuf, keyList);
@@ -140,7 +141,7 @@ void BamRecord::printNull(QuickString &outBuf) const
outBuf.append("\t.\t.\t.\t.\t.\t.", 12);
}
-void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const
+void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyVector *keyList) const
{
outBuf.append('\t');
outBuf.append(_startPosStr);
@@ -156,8 +157,8 @@ void BamRecord::printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyL
vector<int> blockLengths;
vector<int> blockStarts;
- for (RecordKeyList::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
- const Record *block = iter->value();
+ for (RecordKeyVector::const_iterator_type iter = keyList->begin(); iter != keyList->end(); iter = keyList->next()) {
+ const Record *block = *iter;
blockLengths.push_back(block->getEndPos() - block->getStartPos());
blockStarts.push_back(block->getStartPos() - _startPos);
}
diff --git a/src/utils/FileRecordTools/Records/BamRecord.h b/src/utils/FileRecordTools/Records/BamRecord.h
index 074e5ee1d8e5a0a7c34465d3e3fecdf9b40e3702..f3c2494863fa5e9ad480b40c291c57a4db8835ee 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.h
+++ b/src/utils/FileRecordTools/Records/BamRecord.h
@@ -15,7 +15,7 @@
class FileReader;
class BamFileReader;
-class RecordKeyList;
+class RecordKeyVector;
class BamRecord : public Bed6Interval {
public:
@@ -42,11 +42,11 @@ public:
using Bed6Interval::print;
- virtual void print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const;
- virtual void print(QuickString &outBuf, RecordKeyList *keyList) const;
- virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const;
+ virtual void print(QuickString &outBuf, int start, int end, RecordKeyVector *keyList) const;
+ virtual void print(QuickString &outBuf, RecordKeyVector *keyList) const;
+ virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyVector *keyList) const;
virtual void printNull(QuickString &outBuf) const;
- virtual void printRemainingBamFields(QuickString &outBuf, RecordKeyList *keyList) const;
+ virtual void printRemainingBamFields(QuickString &outBuf, RecordKeyVector *keyList) const;
virtual void printUnmapped(QuickString &outBuf) const;
virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::BAM_RECORD_TYPE; }
diff --git a/src/utils/FileRecordTools/Records/Bed3Interval.cpp b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
index e31e43eafa5e5bb2a1b7eeadc9940a5332fe17b5..adc2c6e12f4058226f404d2a947345e46d0033a9 100644
--- a/src/utils/FileRecordTools/Records/Bed3Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed3Interval.cpp
@@ -23,6 +23,7 @@ bool Bed3Interval::initFromFile(FileReader *fileReader)
bool Bed3Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
+ setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
fileReader->getField(1, _startPosStr);
fileReader->getField(2, _endPosStr);
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.cpp b/src/utils/FileRecordTools/Records/BlockMgr.cpp
index 0ef322a9c31f85c8dad221e5e2ac15878b620186..e9465527d687820ad859d003616fb182946a0b07 100644
--- a/src/utils/FileRecordTools/Records/BlockMgr.cpp
+++ b/src/utils/FileRecordTools/Records/BlockMgr.cpp
@@ -30,7 +30,7 @@ BlockMgr::~BlockMgr()
delete _blockRecordsMgr;
}
-void BlockMgr::getBlocks(RecordKeyList &keyList, bool &mustDelete)
+void BlockMgr::getBlocks(RecordKeyVector &keyList, bool &mustDelete)
{
switch (keyList.getKey()->getType()) {
case FileRecordTypeChecker::BED12_RECORD_TYPE:
@@ -50,7 +50,7 @@ void BlockMgr::getBlocks(RecordKeyList &keyList, bool &mustDelete)
-void BlockMgr::getBlocksFromBed12(RecordKeyList &keyList, bool &mustDelete)
+void BlockMgr::getBlocksFromBed12(RecordKeyVector &keyList, bool &mustDelete)
{
const Bed12Interval *keyRecord = static_cast<const Bed12Interval *>(keyList.getKey());
int blockCount = keyRecord->getBlockCount();
@@ -78,7 +78,7 @@ void BlockMgr::getBlocksFromBed12(RecordKeyList &keyList, bool &mustDelete)
mustDelete = true;
}
-void BlockMgr::getBlocksFromBam(RecordKeyList &keyList, bool &mustDelete)
+void BlockMgr::getBlocksFromBam(RecordKeyVector &keyList, bool &mustDelete)
{
const BamRecord *keyRecord = static_cast<const BamRecord *>(keyList.getKey());
const vector<BamTools::CigarOp> &cigarData = keyRecord->getCigarData();
@@ -135,26 +135,26 @@ Record *BlockMgr::allocateAndAssignRecord(const Record *keyRecord, int startPos,
return record;
}
-int BlockMgr::getTotalBlockLength(RecordKeyList &keyList) {
+int BlockMgr::getTotalBlockLength(RecordKeyVector &keyList) {
int sum = 0;
- for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
- const Record *record = iter->value();
+ for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ const Record *record = *iter;
sum += record->getEndPos() - record->getStartPos();
}
return sum;
}
-void BlockMgr::deleteBlocks(RecordKeyList &keyList)
+void BlockMgr::deleteBlocks(RecordKeyVector &keyList)
{
- for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
- _blockRecordsMgr->deleteRecord(iter->value());
+ for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ _blockRecordsMgr->deleteRecord(*iter);
}
- keyList.clearList();
+ keyList.clearVector();
}
-int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList, RecordKeyList &resultList)
+int BlockMgr::findBlockedOverlaps(RecordKeyVector &keyList, RecordKeyVector &hitList, RecordKeyVector &resultList)
{
bool deleteKeyBlocks = false;
if (keyList.empty()) {
@@ -164,8 +164,8 @@ int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList
_overlapBases.clear();
int keyBlocksSumLength = getTotalBlockLength(keyList);
//Loop through every database record the query intersected with
- for (RecordKeyList::const_iterator_type hitListIter = hitList.begin(); hitListIter != hitList.end(); hitListIter = hitList.next()) {
- RecordKeyList hitBlocks(hitListIter->value());
+ for (RecordKeyVector::const_iterator_type hitListIter = hitList.begin(); hitListIter != hitList.end(); hitListIter = hitList.next()) {
+ RecordKeyVector hitBlocks(*hitListIter);
bool deleteHitBlocks = false;
getBlocks(hitBlocks, deleteHitBlocks); //get all blocks for the hit record.
int hitBlockSumLength = getTotalBlockLength(hitBlocks); //get total lentgh of the bocks for the hitRecord.
@@ -173,11 +173,11 @@ int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList
bool hitHasOverlap = false;
//loop through every block of the database record.
- for (RecordKeyList::const_iterator_type hitBlockIter = hitBlocks.begin(); hitBlockIter != hitBlocks.end(); hitBlockIter = hitBlocks.next()) {
+ for (RecordKeyVector::const_iterator_type hitBlockIter = hitBlocks.begin(); hitBlockIter != hitBlocks.end(); hitBlockIter = hitBlocks.next()) {
//loop through every block of the query record.
- for (RecordKeyList::const_iterator_type keyListIter = keyList.begin(); keyListIter != keyList.end(); keyListIter = keyList.next()) {
- const Record *keyBlock = keyListIter->value();
- const Record *hitBlock = hitBlockIter->value();
+ for (RecordKeyVector::const_iterator_type keyListIter = keyList.begin(); keyListIter != keyList.end(); keyListIter = keyList.next()) {
+ const Record *keyBlock = *keyListIter;
+ const Record *hitBlock = *hitBlockIter;
int maxStart = max(keyBlock->getStartPos(), hitBlock->getStartPos());
int minEnd = min(keyBlock->getEndPos(), hitBlock->getEndPos());
@@ -194,9 +194,9 @@ int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList
if ((float) totalHitOverlap / (float)keyBlocksSumLength > _overlapFraction) {
if (_hasReciprocal &&
((float)totalHitOverlap / (float)hitBlockSumLength > _overlapFraction)) {
- resultList.push_back(hitListIter->value());
+ resultList.push_back(*hitListIter);
} else if (!_hasReciprocal) {
- resultList.push_back(hitListIter->value());
+ resultList.push_back(*hitListIter);
}
}
}
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.h b/src/utils/FileRecordTools/Records/BlockMgr.h
index 13b76fa87b299a4325d9143df012365d11ae4d64..c503df634f54a219ca4a722263f149122736654a 100644
--- a/src/utils/FileRecordTools/Records/BlockMgr.h
+++ b/src/utils/FileRecordTools/Records/BlockMgr.h
@@ -14,7 +14,7 @@
//Produce and manage seperate records for the sub-intervals inside the
#include "FileRecordTypeChecker.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
using namespace std;
@@ -26,18 +26,18 @@ public:
~BlockMgr();
// Return value is the number of blocks this main record has been split into.
- void getBlocks(RecordKeyList &keyList, bool &mustDelete);
- void deleteBlocks(RecordKeyList &keyList);
+ void getBlocks(RecordKeyVector &keyList, bool &mustDelete);
+ void deleteBlocks(RecordKeyVector &keyList);
// Get the sum of the lengths of all blocks for a record.
- int getTotalBlockLength(RecordKeyList &keyList);
+ int getTotalBlockLength(RecordKeyVector &keyList);
// Determine which hits in the hitList intersect the hits in the keyList by comparing all blocks in each
// and checking that their total intersection meets any overlapFraction and reciprocal criteria compared to
// the total block lengths of the hitList and keyList. All hits that pass will be in the resultList.
// Return value is the number of hits in the result set.
- int findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList, RecordKeyList &resultList);
+ int findBlockedOverlaps(RecordKeyVector &keyList, RecordKeyVector &hitList, RecordKeyVector &resultList);
//these are setting options for splitting BAM records
void setBreakOnDeletionOps(bool val) { _breakOnDeletionOps = val; }
@@ -57,8 +57,8 @@ private:
// For now, all records will be split into Bed6 records.
const static FileRecordTypeChecker::RECORD_TYPE _blockRecordsType = FileRecordTypeChecker::BED6_RECORD_TYPE;
- void getBlocksFromBed12(RecordKeyList &keyList, bool &mustDelete);
- void getBlocksFromBam(RecordKeyList &keyList, bool &mustDelete);
+ void getBlocksFromBed12(RecordKeyVector &keyList, bool &mustDelete);
+ void getBlocksFromBam(RecordKeyVector &keyList, bool &mustDelete);
Record *allocateAndAssignRecord(const Record *keyRecord, int startPos, int endPos);
diff --git a/src/utils/FileRecordTools/Records/GffRecord.cpp b/src/utils/FileRecordTools/Records/GffRecord.cpp
index 21cea1dab87ea07e05e5b6331ecca4f9abe56cb5..b80d2d19b82d747670bae2955f28c2c1510fc388 100644
--- a/src/utils/FileRecordTools/Records/GffRecord.cpp
+++ b/src/utils/FileRecordTools/Records/GffRecord.cpp
@@ -23,6 +23,7 @@ void GffRecord::clear()
bool GffRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
+ setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
fileReader->getField(3, _startPosStr);
_startPos = str2chrPos(_startPosStr);
diff --git a/src/utils/FileRecordTools/Records/Makefile b/src/utils/FileRecordTools/Records/Makefile
index f471e666f110fa39f3cc4dde99b879ec580e07f1..14e03c60810eb2460e294aba562e1f454e26302d 100644
--- a/src/utils/FileRecordTools/Records/Makefile
+++ b/src/utils/FileRecordTools/Records/Makefile
@@ -17,13 +17,14 @@ INCLUDES = -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= RecordMgr.cpp RecordMgr.h Record.h Record.cpp EmptyRecord.h EmptyRecord.cpp Bed3Interval.h Bed3Interval.cpp \
+SOURCES = Record.h Record.cpp EmptyRecord.h EmptyRecord.cpp Bed3Interval.h Bed3Interval.cpp \
Bed4Interval.h Bed4Interval.cpp BedGraphInterval.h BedGraphInterval.cpp Bed5Interval.h Bed5Interval.cpp \
Bed6Interval.h Bed6Interval.cpp \
BedPlusInterval.h BedPlusInterval.cpp Bed12Interval.h Bed12Interval.cpp BamRecord.h BamRecord.cpp VcfRecord.h VcfRecord.cpp \
- GffRecord.h GffRecord.cpp RecordKeyList.h RecordKeyList.cpp BlockMgr.h BlockMgr.cpp StrandQueue.h StrandQueue.cpp
-OBJECTS= RecordMgr.o Record.o EmptyRecord.o Bed3Interval.o Bed4Interval.o BedGraphInterval.o Bed5Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
- VcfRecord.o GffRecord.o RecordKeyList.o BlockMgr.o StrandQueue.o
+ GffRecord.h GffRecord.cpp BlockMgr.h BlockMgr.cpp StrandQueue.h StrandQueue.cpp \
+ RecordMgr.cpp RecordMgr.h RecordList.h RecordList.cpp RecordKeyList.h RecordKeyList.cpp RecordKeyVector.h RecordKeyVector.cpp
+OBJECTS= Record.o EmptyRecord.o Bed3Interval.o Bed4Interval.o BedGraphInterval.o Bed5Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
+ VcfRecord.o GffRecord.o BlockMgr.o StrandQueue.o RecordMgr.o RecordList.o RecordKeyList.o RecordKeyVector.o
_EXT_OBJECTS=ParseTools.o QuickString.o ChromIdLookup.o
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
@@ -38,8 +39,9 @@ $(BUILT_OBJECTS): $(SOURCES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/RecordMgr.o $(OBJ_DIR)/Record.o $(OBJ_DIR)/EmptyRecord.o $(OBJ_DIR)/Bed3Interval.o $(OBJ_DIR)/Bed4Interval.o \
+ @rm -f $(OBJ_DIR)/RecordMgr.o $(OBJ_DIR)/RecordList.o $(OBJ_DIR)/Record.o $(OBJ_DIR)/EmptyRecord.o $(OBJ_DIR)/Bed3Interval.o $(OBJ_DIR)/Bed4Interval.o \
$(OBJ_DIR)/BedGraphInterval.o $(OBJ_DIR)/Bed5Interval.o $(OBJ_DIR)/Bed6Interval.o \
- $(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o $(OBJ_DIR)/StrandQueue.o
+ $(OBJ_DIR)/BedPlusInterval.o $(OBJ_DIR)/Bed12Interval.o $(OBJ_DIR)/BamRecord.o $(OBJ_DIR)/VcfRecord.o $(OBJ_DIR)/GffRecord.o $(OBJ_DIR)/BlockMgr.o $(OBJ_DIR)/StrandQueue.o \
+ $(OBJ_DIR)/RecordKeyList.o $(OBJ_DIR)/RecordKeyVector.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index 89544ed21f23e91d7db73ab1e6e2158edc695ae9..2499ce28cad9cbdc3fc25a7fb7c11853ba95a45d 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -3,7 +3,8 @@
#include <cstdio>
Record::Record()
-: _chrId(-1),
+: _fileIdx(-1),
+ _chrId(-1),
_startPos(-1),
_endPos(-1),
_strandVal(UNKNOWN),
@@ -18,6 +19,7 @@ Record::~Record() {
const Record &Record::operator=(const Record &other)
{
+ _fileIdx = other._fileIdx;
_chrName = other._chrName;
_chrId = other._chrId;
_startPos = other._startPos;
@@ -29,6 +31,7 @@ const Record &Record::operator=(const Record &other)
}
void Record::clear() {
+ _fileIdx = -1;
_chrName.clear();
_chrId = -1;
_startPos = -1;
@@ -72,6 +75,35 @@ bool Record::operator > (const Record &other) const {
return false;
}
+bool Record::lessThan(const Record *other) const
+{
+ if (!sameChrom(other)) {
+ return chromBefore(other);
+ }
+ if (_startPos != other->_startPos) {
+ return _startPos < other->_startPos;
+ }
+ if (_endPos != other->_endPos) {
+ return _endPos < other->_endPos;
+ }
+ return false;
+}
+
+bool Record::greaterThan(const Record *other) const
+{
+ if (!sameChrom(other)) {
+ return chromAfter(other);
+ }
+ if (_startPos != other->_startPos) {
+ return _startPos > other->_startPos;
+ }
+ if (_endPos != other->_endPos) {
+ return _endPos > other->_endPos;
+ }
+ return false;
+
+}
+
bool Record::sameChrom(const Record *other) const {
return (_chrId == -1 || other->_chrId == -1) ? ( _chrName == other->_chrName) : (_chrId == other->_chrId);
}
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 5adbc787035c551c9d8910cb1687453469b830ab..75b7dd655de451ed0997117c00c230bc3aab26f9 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -43,6 +43,8 @@ public:
virtual void setChrName(const string &chr) { _chrName = chr; }
virtual void setChrName(const char *chr) { _chrName = chr; }
+ virtual int getFileIdx() const { return _fileIdx; }
+ virtual void setFileIdx(int fileIdx) { _fileIdx = fileIdx; }
virtual int getChromId() const { return _chrId; }
virtual void setChromId(int id) { _chrId = id; }
@@ -110,7 +112,8 @@ public:
virtual bool operator < (const Record &other) const;
virtual bool operator > (const Record &other) const;
-
+ virtual bool lessThan(const Record *other) const;
+ virtual bool greaterThan(const Record *other) const;
//is this on the same chromosome as another record?
bool sameChrom(const Record *other) const;
@@ -136,6 +139,7 @@ public:
protected:
virtual ~Record(); //by making the destructor protected, only the friend class(es) can actually delete Record objects, or objects derived from Record.
+ int _fileIdx; //associated file the record came from
QuickString _chrName;
int _chrId;
int _startPos;
@@ -153,9 +157,13 @@ protected:
bool _isMateUnmapped;
};
-class RecordPtrSortFunctor {
+class RecordPtrSortAscFunctor {
public:
- bool operator()(const Record *rec1, const Record *rec2) const { return *rec1 > *rec2; }
+ bool operator()(const Record *rec1, const Record *rec2) const { return *rec1 < *rec2; }
};
+class RecordPtrSortDescFunctor {
+public:
+ bool operator()(const Record *rec1, const Record *rec2) const { return *rec1 > *rec2; }
+};
#endif /* RECORD_H_ */
diff --git a/src/utils/FileRecordTools/Records/RecordKeyList.h b/src/utils/FileRecordTools/Records/RecordKeyList.h
index 948f677b0f6e427c3559ca60ae9e7732d7ed85a3..6c0a3fcaeff1b7a561e4ecc2efe3fe0139c2e48f 100644
--- a/src/utils/FileRecordTools/Records/RecordKeyList.h
+++ b/src/utils/FileRecordTools/Records/RecordKeyList.h
@@ -9,13 +9,13 @@
#define KEYLIST_H_
#include "Record.h"
-#include "BTlist.h"
+#include "RecordList.h"
class RecordKeyList {
public:
typedef const Record * elemType;
- typedef BTlist<elemType> listType;
- typedef const BTlistNode<elemType> *const_iterator_type;
+ typedef RecordList listType;
+ typedef const RecordListNode *const_iterator_type;
RecordKeyList();
RecordKeyList(elemType item);
RecordKeyList(elemType item, const listType &list);
@@ -45,6 +45,8 @@ public:
}
bool allClear() { return (_key == NULL && empty()); }
+ void sort() { _list.sort(); }
+
private:
elemType _key;
diff --git a/src/utils/FileRecordTools/Records/RecordKeyVector.cpp b/src/utils/FileRecordTools/Records/RecordKeyVector.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..e1110ffc3678806bcd2c8a91ed8e9324a055d305
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordKeyVector.cpp
@@ -0,0 +1,88 @@
+/*
+ * RecordKeyVector.cpp
+ *
+ * Created on: Aug 1, 2014
+ * Author: nek3d
+ */
+
+
+#include "RecordKeyVector.h"
+#include <algorithm>
+
+RecordKeyVector::RecordKeyVector()
+: _key(NULL),
+ _currPos(0)
+{
+}
+
+RecordKeyVector::RecordKeyVector(const Record * item)
+: _key(item),
+ _currPos(0)
+{
+}
+
+RecordKeyVector::RecordKeyVector(const Record * item, const vecType &vec)
+: _key(item),
+ _currPos(0)
+{
+ _recVec = vec;
+}
+
+RecordKeyVector::~RecordKeyVector() {
+}
+
+const RecordKeyVector &RecordKeyVector::operator=(const RecordKeyVector &other)
+{
+ setKey(other._key);
+ _recVec = other._recVec;
+ return *this;
+}
+
+const RecordKeyVector::const_iterator_type RecordKeyVector::begin() {
+ _currPos = 0;
+ return _recVec.begin();
+}
+
+const RecordKeyVector::const_iterator_type RecordKeyVector::next() {
+ _currPos++;
+ return _recVec.begin() + _currPos;
+}
+
+
+const RecordKeyVector::const_iterator_type RecordKeyVector::end() {
+ return _recVec.end();
+}
+
+size_t RecordKeyVector::size() const {
+ return _recVec.size();
+}
+
+bool RecordKeyVector::empty() const {
+ return _recVec.empty();
+}
+
+void RecordKeyVector::push_back(elemType item) {
+ _recVec.push_back(item);
+}
+
+const Record *RecordKeyVector::getKey() const {
+ return _key;
+}
+
+void RecordKeyVector::setKey(elemType key) {
+ _key = key;
+}
+
+void RecordKeyVector::setVector(const vecType &vec) {
+ _recVec = vec;
+}
+
+void RecordKeyVector::clearVector() {
+ _recVec.clear();
+}
+
+void RecordKeyVector::sortVector() {
+ std::sort(_recVec.begin(), _recVec.end(), RecordPtrSortAscFunctor());
+}
+
+
diff --git a/src/utils/FileRecordTools/Records/RecordKeyVector.h b/src/utils/FileRecordTools/Records/RecordKeyVector.h
new file mode 100644
index 0000000000000000000000000000000000000000..a7389d52cf9c1503171cd80f898172117e2e2bbd
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordKeyVector.h
@@ -0,0 +1,63 @@
+/*
+ * RecordKeyVector.h
+ *
+ * Created on: Dec 14, 2012
+ * Author: nek3d
+ */
+
+#ifndef KEYVECTOR_H_
+#define KEYVECTOR_H_
+
+
+
+
+using namespace std;
+
+#include "Record.h"
+#include <vector>
+
+class RecordKeyVector {
+public:
+ typedef const Record * elemType;
+ typedef vector<const Record *> vecType;
+ typedef vecType::const_iterator const_iterator_type;
+ RecordKeyVector();
+ RecordKeyVector(elemType item);
+ RecordKeyVector(elemType item, const vecType &vector);
+ ~RecordKeyVector();
+
+ const RecordKeyVector &operator=(const RecordKeyVector &other);
+ const const_iterator_type begin();
+ const const_iterator_type next();
+ const const_iterator_type end();
+ size_t size() const ;
+ bool empty() const ; //only checks whether list is empty. Doesn't check key.
+ void push_back(elemType item);
+ elemType getKey() const ;
+ void setKey(elemType key);
+
+ //setVectorNoCopy will make our list share the nodes of another
+ //list, not copy them.
+ void setVector(const vecType &list);
+
+ // WARNING! clearVector will NOT delete records pointed to by list nodes. Caller must do that separately, since the RecordKeyVector
+ // does not have it's own RecordMgr member.
+ void clearVector();
+
+ void clearAll() {
+ setKey(NULL);
+ clearVector();
+ }
+ bool allClear() { return (_key == NULL && empty()); }
+
+ void sortVector();
+
+
+private:
+ elemType _key;
+ vecType _recVec;
+ int _currPos;
+};
+
+
+#endif /* RECORDKEYLIST_H_ */
diff --git a/src/utils/FileRecordTools/Records/RecordList.cpp b/src/utils/FileRecordTools/Records/RecordList.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..142706fd312ece5fa6b2641ba9488a929915be1f
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordList.cpp
@@ -0,0 +1,202 @@
+/*
+ * RecordList.cpp
+ *
+ * Created on: Jun 19, 2014
+ * Author: nek3d
+ */
+
+#include "RecordList.h"
+
+RecordList::RecordList() :
+ _begin(NULL),
+ _currEnd(NULL),
+ _prevCursor(NULL),
+ _size(0),
+ _dontDelete(false)
+{
+}
+
+void RecordList::pop_front() {
+ if (empty()) {
+ return;
+ }
+ RecordListNode *killNode = _begin;
+ if (_begin->_next == NULL) { //this is the only item. List size is 1.
+ delete killNode;
+ _begin = NULL;
+ _currEnd = NULL;
+ _prevCursor = NULL;
+ _size = 0;
+ return;
+ }
+ if (_prevCursor == _begin) {
+ _prevCursor = _begin->_next;
+ }
+ _begin = _begin->next();
+ delete killNode;
+ _size--;
+}
+
+const RecordListNode *RecordList::next() {
+ if (_prevCursor == NULL) {
+ _prevCursor = _begin;
+ return _begin->_next;
+ }
+ _prevCursor = _prevCursor->_next;
+ return _prevCursor->_next;
+}
+
+
+RecordListNode *RecordList::deleteCurrent() {
+ //delete what the current cursor is pointing to,
+ //meaning whatever the prevCursor's next member points to.
+ RecordListNode *returnNode = NULL;
+ RecordListNode *killNode = NULL;
+ if (_prevCursor == NULL) {
+ //deleting first item in list.
+ killNode = _begin;
+ _begin = _begin->_next;
+ returnNode = _begin;
+
+ } else {
+ killNode = _prevCursor->_next;
+ _prevCursor->_next = _prevCursor->_next->_next;
+ returnNode = _prevCursor->_next;
+ }
+ if (_currEnd == killNode) {
+ //deleting last item in list
+ _currEnd = _prevCursor; //back up the current end.
+ }
+ delete killNode;
+ _size--;
+
+ return returnNode;
+}
+
+void RecordList::push_back(const Record * &val) {
+ RecordListNode *newNode = new RecordListNode(val);
+ if (empty()) {
+ _begin = newNode;
+ _currEnd = newNode;
+ _prevCursor = NULL;
+ } else {
+ _currEnd->_next = newNode;
+ _prevCursor = _currEnd;
+ _currEnd = newNode;
+ }
+ _size++;
+}
+
+
+void RecordList::clear() {
+ if (_dontDelete) {
+ return;
+ }
+ //delete all nodes, set cursors to NULL, set size to 0.
+ RecordListNode *killNode = _begin;
+ while (killNode != NULL) {
+ RecordListNode *nextNode = killNode->_next;
+ delete killNode;
+ killNode = nextNode;
+ }
+ _begin = NULL;
+ _currEnd = NULL;
+ _prevCursor = NULL;
+ _size = 0;
+}
+
+const RecordList &RecordList::operator=(const RecordList &other) {
+ //need to make copies of all nodes and assign values
+ clear();
+
+ RecordListNode *node = other._begin;
+ while (node != NULL) {
+ push_back(node->_val);
+ node = node->_next;
+ }
+ return *this;
+}
+void RecordList::assignNoCopy(RecordList &other) {
+ _begin = other._begin;
+ _size = other._size;
+ _currEnd = other._currEnd;
+ _prevCursor = other._prevCursor;
+ _dontDelete = true;
+}
+
+
+void RecordList::mergeSort(RecordListNode **headRef) {
+ RecordListNode *head = *headRef;
+ RecordListNode *a;
+ RecordListNode *b;
+
+ /* Base case -- length 0 or 1 */
+ if ((head == NULL) || (head->_next == NULL)) {
+ return;
+ }
+
+ /* Split head into 'a' and 'b' sublists */
+ frontBackSplit(head, &a, &b);
+
+ /* Recursively sort the sublists */
+ mergeSort(&a);
+ mergeSort(&b);
+
+ /* answer = merge the two sorted lists together */
+ *headRef = sortedMerge(a, b);
+}
+
+RecordListNode* RecordList::sortedMerge(RecordListNode * a, RecordListNode * b) {
+ RecordListNode *result = NULL;
+
+ /* Base cases */
+ if (a == NULL) return(b);
+ else if (b==NULL) return(a);
+
+ /* Pick either a or b, and recur */
+ if (a->_val->lessThan(b->_val)) {
+ result = a;
+ result->_next = sortedMerge(a->_next, b);
+ } else {
+ result = b;
+ result->_next = sortedMerge(a, b->_next);
+ }
+ return(result);
+}
+
+/* URecord *ILIRecord *Y FUNCRecord *IONS */
+/* Split the nodes of the given list into front and back halves,
+ and return the two lists using the reference parameters.
+ If the length is odd, the extra node should go in the front list.
+ Uses the fast/slow pointer strategy. */
+void RecordList::frontBackSplit(RecordListNode* source,
+ RecordListNode** frontRef, RecordListNode** backRef) {
+ RecordListNode *fast;
+ RecordListNode *slow;
+ if (source==NULL || source->_next==NULL) {
+ /* length < 2 cases */
+ *frontRef = source;
+ *backRef = NULL;
+ } else {
+ slow = source;
+ fast = source->_next;
+
+ /* Advance 'fast' two nodes, and advance 'slow' one node */
+ while (fast != NULL) {
+ fast = fast->_next;
+ if (fast != NULL) {
+ slow = slow->_next;
+ fast = fast->_next;
+ }
+ }
+
+ /* 'slow' is before the midpoint in the list, so split it in two
+ at that point. */
+ *frontRef = source;
+ *backRef = slow->_next;
+ slow->_next = NULL;
+ }
+}
+
+
+
diff --git a/src/utils/FileRecordTools/Records/RecordList.h b/src/utils/FileRecordTools/Records/RecordList.h
new file mode 100644
index 0000000000000000000000000000000000000000..e1b24b562ec08797baeeaa664eec0749b539c223
--- /dev/null
+++ b/src/utils/FileRecordTools/Records/RecordList.h
@@ -0,0 +1,117 @@
+/*
+ * RecordListPtr.h
+ *
+ * Created on: Jun 19, 2014
+ * Author: nek3d
+ */
+
+#ifndef RECORD_LIST_H_
+#define RECORD_LIST_H_
+
+
+// Writing our own singly linked list class because:
+//
+// 1) SRecord *L doesn't currently support one that I can find without
+// C++0x support or SGI extensions.
+//
+// 2) A normal singly linked list doesn't support constant time
+// insertion or deletion at the end. It also doesn't track
+// your current position or let you delete at that position,
+// but this does.
+//
+// 3) A normal SRecord *L list is doubly-linked, which would do all
+// these things, but more slowly and with more memory.
+//
+// 4) I can.
+
+
+#include "FreeList.h"
+#include "QuickString.h"
+#include <cstring> //for memset
+#include "Record.h"
+
+class RecordListNode {
+public:
+ friend class RecordList;
+
+ RecordListNode() : _next(NULL){}
+ RecordListNode(const Record * val) : _val(val), _next(NULL) {}
+ const Record * value() const { return _val; }
+ const RecordListNode *next() const { return _next; }
+ RecordListNode *next() { return _next; }
+ bool hasNext() const { return _next != NULL; }
+ void clear() {
+ _next = NULL;
+ _val = NULL; // WARNING! Since _val is a pointer,
+ // the user is responsible for any needed deallocation.
+ }
+
+private:
+
+ const Record * _val;
+ RecordListNode *_next;
+};
+
+class RecordList {
+public:
+ RecordList();
+
+ ~RecordList() { clear(); }
+
+ typedef const RecordListNode * const_iterator_type;
+
+ bool empty() const { return _begin == NULL; }
+ size_t size() const { return _size; }
+
+ const RecordListNode *front() const { return _begin;}
+ RecordListNode *back() const { return _currEnd; }
+ void pop_front();
+ const RecordListNode *begin() {
+ _prevCursor = NULL;
+ return _begin;
+ }
+
+ const RecordListNode *begin() const { return _begin; }
+ const RecordListNode *next();
+ const RecordListNode *end() const { return NULL; }
+
+ RecordListNode * deleteCurrent();
+ void push_back(const Record * &val);
+
+ void clear();
+ const RecordList &operator=(const RecordList &other);
+ void assignNoCopy(RecordList &other);
+
+ void sort() { mergeSort(&_begin); }
+
+private:
+ RecordListNode *_begin;
+ //keep a cursor to the last element for constant time push_back and pop_back functions.
+ RecordListNode *_currEnd;
+ RecordListNode *_prevCursor;
+ size_t _size;
+
+ bool _dontDelete; //this will usally be false, but set to true when
+ //calling assignNoCopy, as our list will actually just be a pointer
+ //to another list.
+
+
+
+ // The rest of this is just helper methods for sorting.
+ // We'll use a mergeSort for optimal time / space efficiency.
+ // The following methods are copied almost verbatim from
+ // http://www.geeksforgeeks.org/merge-sort-for-linked-list/
+
+ void mergeSort(RecordListNode **headRef);
+ RecordListNode* sortedMerge(RecordListNode * a, RecordListNode * b);
+
+ /* Split the nodes of the given list into front and back halves,
+ and return the two lists using the reference parameters.
+ If the length is odd, the extra node should go in the front list.
+ Uses the fast/slow pointer strategy. */
+ void frontBackSplit(RecordListNode* source,
+ RecordListNode** frontRef, RecordListNode** backRef);
+};
+
+
+#endif /* RECORD_LIST_H_ */
diff --git a/src/utils/FileRecordTools/Records/StrandQueue.h b/src/utils/FileRecordTools/Records/StrandQueue.h
index bd02b4090fc4577bc85425f27bcba8019b0f8cf5..f20e1a1c1454e3928076330d92e27f80ddfdcc33 100644
--- a/src/utils/FileRecordTools/Records/StrandQueue.h
+++ b/src/utils/FileRecordTools/Records/StrandQueue.h
@@ -30,7 +30,7 @@ public:
private:
// static RecordPtrSortFunctor _recSortFunctor;
- typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortFunctor > queueType;
+ typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortDescFunctor > queueType;
vector<queueType *> _queues;
static const int NUM_QUEUES = 3;
diff --git a/src/utils/FileRecordTools/Records/VcfRecord.cpp b/src/utils/FileRecordTools/Records/VcfRecord.cpp
index 20cbb6f7cf881f8af7a3f468cb73ce96e21210dc..b3ac4666a89fde61db2e1904512638734450ab2d 100644
--- a/src/utils/FileRecordTools/Records/VcfRecord.cpp
+++ b/src/utils/FileRecordTools/Records/VcfRecord.cpp
@@ -10,6 +10,7 @@
bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
{
+ setFileIdx(fileReader->getFileIdx());
fileReader->getField(0, _chrName);
_chrId = fileReader->getCurrChromdId();
fileReader->getField(1, _startPosStr);
@@ -32,8 +33,8 @@ bool VcfRecord::initFromFile(SingleLineDelimTextFileReader *fileReader)
void VcfRecord::clear()
{
BedPlusInterval::clear();
- _varAlt.clear();
- _varRef.clear();
+ _varAlt.release();
+ _varRef.release();
}
void VcfRecord::print(QuickString &outBuf) const {
diff --git a/src/utils/GenomeFile/NewGenomeFile.cpp b/src/utils/GenomeFile/NewGenomeFile.cpp
index 84e44cbed97dcdbd7c0fdb760dc02edca634bad8..8d7af4d88abf514f6e0570d1210ebda7cb007e5c 100644
--- a/src/utils/GenomeFile/NewGenomeFile.cpp
+++ b/src/utils/GenomeFile/NewGenomeFile.cpp
@@ -23,12 +23,20 @@ NewGenomeFile::NewGenomeFile(const QuickString &genomeFilename)
NewGenomeFile::NewGenomeFile(const BamTools::RefVector &refVector)
: _maxId(-1)
{
- for (size_t i = 0; i < refVector.size(); ++i) {
+ size_t i = 0;
+ for (; i < refVector.size(); ++i) {
QuickString chrom = refVector[i].RefName;
CHRPOS length = refVector[i].RefLength;
_maxId++;
_chromSizeIds[chrom] = pair<CHRPOS, CHRPOS>(length, _maxId);
+ _chromList.push_back(chrom);
}
+ // Special: BAM files can have unmapped reads, which show as no chromosome, or an empty chrom string.
+ // Add in an empty chrom so these don't error.
+ _maxId++;
+ _chromSizeIds[""] = pair<CHRPOS, int>(0, _maxId);
+ _chromList.push_back("");
+
}
// Destructor
@@ -69,6 +77,13 @@ void NewGenomeFile::loadGenomeFileIntoMap() {
cerr << "Error: The genome file " << _genomeFileName << " has no valid entries. Exiting." << endl;
exit(1);
}
+ // Special: BAM files can have unmapped reads, which show as no chromosome, or an empty chrom string.
+ // Add in an empty chrom so these don't error.
+ _maxId++;
+ _chromSizeIds[""] = pair<CHRPOS, int>(0, _maxId);
+ _chromList.push_back("");
+
+
_startOffsets.push_back(_genomeLength); //insert the final length as the last element
//to help with the lower_bound call in the projectOnGenome method.
genFile.close();
diff --git a/src/utils/GenomeFile/NewGenomeFile.h b/src/utils/GenomeFile/NewGenomeFile.h
index 99a97fab46d9f63d7548ecb8efecb9c56b1dad72..7b804a6c51f06daef36bfc8e135d542df1e8a483 100644
--- a/src/utils/GenomeFile/NewGenomeFile.h
+++ b/src/utils/GenomeFile/NewGenomeFile.h
@@ -38,7 +38,7 @@ public:
CHRPOS getChromSize(const QuickString &chrom); // return the size of a chromosome
CHRPOS getChromId(const QuickString &chrom); // return chromosome's sort order
const vector<QuickString> &getChromList() const { return _chromList; } // return a list of chrom names
- CHRPOS getNumberOfChroms() const { return _chromList.size(); }
+ CHRPOS getNumberOfChroms() const { return _chromList.size() -1; }//the -1 excludes the blank chrom added for unmapped reads
const QuickString &getGenomeFileName() const { return _genomeFileName; }
diff --git a/src/utils/KeyListOps/KeyListOps.cpp b/src/utils/KeyListOps/KeyListOps.cpp
index 15ec3fda48f3b2579721d40a5520e0bbad97c2bf..531654896363d82a5909f62edf0d5928f03e8b5b 100644
--- a/src/utils/KeyListOps/KeyListOps.cpp
+++ b/src/utils/KeyListOps/KeyListOps.cpp
@@ -154,7 +154,7 @@ bool KeyListOps::isValidColumnOps(FileRecordMgr *dbFile) {
return true;
}
-const QuickString & KeyListOps::getOpVals(RecordKeyList &hits)
+const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
{
//loop through all requested columns, and for each one, call the method needed
//for the operation specified.
diff --git a/src/utils/KeyListOps/KeyListOps.h b/src/utils/KeyListOps/KeyListOps.h
index b2137d87d8f1e80b4389e7291169d50823f2838d..8262677cd133fe4122be1481c7bb1916e4034e85 100644
--- a/src/utils/KeyListOps/KeyListOps.h
+++ b/src/utils/KeyListOps/KeyListOps.h
@@ -40,7 +40,7 @@ public:
const QuickString &getNullValue() { return _methods.getNullValue(); }
const QuickString &getDelimStr() { return _methods.getDelimStr(); }
- void setKeyList(RecordKeyList *keyList) { _methods.setKeyList(keyList); }
+ void setKeyList(RecordKeyVector *keyList) { _methods.setKeyList(keyList); }
typedef enum { SUM, MEAN, STDDEV, SAMPLE_STDDEV, MEDIAN, MODE, ANTIMODE, MIN, MAX, ABSMIN, ABSMAX, COUNT, DISTINCT, COUNT_DISTINCT,
DISTINCT_ONLY, COLLAPSE, CONCAT, FREQ_ASC, FREQ_DESC, FIRST, LAST, INVALID } OP_TYPES;
@@ -48,7 +48,7 @@ public:
void setDBfileType(FileRecordTypeChecker::FILE_TYPE type) { _dbFileType = type; }
bool isValidColumnOps(FileRecordMgr *dbFile);
- const QuickString &getOpVals(RecordKeyList &hits);
+ const QuickString &getOpVals(RecordKeyVector &hits);
private:
void init();
diff --git a/src/utils/KeyListOps/KeyListOpsMethods.cpp b/src/utils/KeyListOps/KeyListOpsMethods.cpp
index cd649faae463f7d8ad5d49a86444ee3205241484..028471ae791ce2ed29e2b334de5098ec51f72b77 100644
--- a/src/utils/KeyListOps/KeyListOpsMethods.cpp
+++ b/src/utils/KeyListOps/KeyListOpsMethods.cpp
@@ -22,7 +22,7 @@ KeyListOpsMethods::KeyListOpsMethods()
{
}
-KeyListOpsMethods::KeyListOpsMethods(RecordKeyList *keyList, int column)
+KeyListOpsMethods::KeyListOpsMethods(RecordKeyVector *keyList, int column)
: _keyList(keyList),
_column(column),
_nullVal("."),
@@ -313,13 +313,13 @@ const QuickString &KeyListOpsMethods::getLast() {
}
const QuickString &KeyListOpsMethods::getColVal() {
- const QuickString &retVal = _iter->value()->getField(_column);
+ const QuickString &retVal = (*_iter)->getField(_column);
if (_isBam && retVal.empty()) return _nullVal;
return retVal;
}
double KeyListOpsMethods::getColValNum() {
- const QuickString &strVal = _iter->value()->getField(_column);
+ const QuickString &strVal = (*_iter)->getField(_column);
if (!isNumeric(strVal)) {
_nonNumErrFlag = true;
_errMsg = " ***** WARNING: Non numeric value ";
diff --git a/src/utils/KeyListOps/KeyListOpsMethods.h b/src/utils/KeyListOps/KeyListOpsMethods.h
index 16796858841eea0524015dd9c0073e641c5ecab6..fbf5101214a4c7ae749f2a4298e6981c332be738 100644
--- a/src/utils/KeyListOps/KeyListOpsMethods.h
+++ b/src/utils/KeyListOps/KeyListOpsMethods.h
@@ -12,18 +12,18 @@
#include <utility> //for pair
#include "QuickString.h"
#include <stdint.h>
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
using namespace std;
class KeyListOpsMethods {
public:
KeyListOpsMethods();
- KeyListOpsMethods(RecordKeyList *keyList, int column = 1);
+ KeyListOpsMethods(RecordKeyVector *keyList, int column = 1);
~KeyListOpsMethods();
void setIsBam(bool isBam) { _isBam = isBam; }
- void setKeyList(RecordKeyList *keyList) { _keyList = keyList; }
+ void setKeyList(RecordKeyVector *keyList) { _keyList = keyList; }
void setColumn(int col) { _column = col; }
void setNullValue(const QuickString & nullVal) { _nullVal = nullVal; }
const QuickString &getNullValue() const { return _nullVal; }
@@ -81,14 +81,14 @@ public:
}
private:
- RecordKeyList *_keyList;
+ RecordKeyVector *_keyList;
int _column;
QuickString _nullVal;
QuickString _delimStr;
QuickString _retStr;
- RecordKeyList _nullKeyList; //this has to exist just so we can initialize _iter, below.
- RecordKeyList::const_iterator_type _iter;
+ RecordKeyVector _nullKeyList; //this has to exist just so we can initialize _iter, below.
+ RecordKeyVector::const_iterator_type _iter;
// Some methods need to put values into a vector, mostly for sorting.
vector<double> _numArray;
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index 34647d678c448ccdfefbe32adcd856a81476b58b..f7561e8c139087b72a1755efe2abf7373088179a 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -18,32 +18,35 @@ NewChromSweep::NewChromSweep(ContextIntersect *context,
bool useMergedIntervals)
: _context(context),
_queryFRM(NULL),
- _databaseFRM(NULL),
- _useMergedIntervals(false),
+ _numDBs(_context->getNumDatabaseFiles()),
+ _useMergedIntervals(false),
_queryRecordsTotalLength(0),
_databaseRecordsTotalLength(0),
_wasInitialized(false),
_currQueryRec(NULL),
- _currDatabaseRec(NULL),
_runToQueryEnd(false)
-
{
}
bool NewChromSweep::init() {
- //Create new FileRecordMgrs for the two input files.
+ //Create new FileRecordMgrs for the input files.
//Open them, and get the first record from each.
- //if any of that goes wrong, return false;
//otherwise, return true.
_queryFRM = _context->getFile(_context->getQueryFileIdx());
- _databaseFRM = _context->getFile(_context->getDatabaseFileIdx());
- nextRecord(false);
-// if (_currDatabaseRec == NULL) {
-// return false;
-// }
+ _dbFRMs.resize(_numDBs, NULL);
+ for (int i=0; i < _numDBs; i++) {
+ _dbFRMs[i] = _context->getDatabaseFile(i);
+ }
+
+ _currDbRecs.resize(_numDBs, NULL);
+ for (int i=0; i < _numDBs; i++) {
+ nextRecord(false, i);
+ }
+
+ _caches.resize(_numDBs);
//determine whether to stop when the database end is hit, or keep going until the
//end of the query file is hit as well.
@@ -59,9 +62,12 @@ void NewChromSweep::closeOut() {
while (!_queryFRM->eof()) {
nextRecord(true);
}
- while (!_databaseFRM->eof()) {
- nextRecord(false);
- }
+
+ for (int i=0; i < _numDBs; i++) {
+ while (!_dbFRMs[i]->eof()) {
+ nextRecord(false, i);
+ }
+ }
}
NewChromSweep::~NewChromSweep(void) {
@@ -71,136 +77,147 @@ NewChromSweep::~NewChromSweep(void) {
_queryFRM->deleteRecord(_currQueryRec);
_currQueryRec = NULL;
- _databaseFRM->deleteRecord(_currDatabaseRec);
- _currDatabaseRec = NULL;
+
+ for (int i=0; i < _numDBs; i++) {
+ _dbFRMs[i]->deleteRecord(_currDbRecs[i]);
+ _currDbRecs[i] = NULL;
+ }
_queryFRM->close();
- _databaseFRM->close();
+
+ for (int i=0; i < _numDBs; i++) {
+ _dbFRMs[i]->close();
+ }
}
-void NewChromSweep::scanCache() {
- recListIterType cacheIter = _cache.begin();
- while (cacheIter != _cache.end())
+void NewChromSweep::scanCache(int dbIdx, RecordKeyVector &retList) {
+ recListIterType cacheIter = _caches[dbIdx].begin();
+ while (cacheIter != _caches[dbIdx].end())
{
const Record *cacheRec = cacheIter->value();
if (_currQueryRec->sameChrom(cacheRec) && !(_currQueryRec->after(cacheRec))) {
if (intersects(_currQueryRec, cacheRec)) {
- _hits.push_back(cacheRec);
- }
- cacheIter = _cache.next();
+ retList.push_back(cacheRec);
+ } else break; // cacheRec is after the query rec, stop scanning.
+ cacheIter = _caches[dbIdx].next();
}
else {
- cacheIter = _cache.deleteCurrent();
- _databaseFRM->deleteRecord(cacheRec);
+ cacheIter = _caches[dbIdx].deleteCurrent();
+ _dbFRMs[dbIdx]->deleteRecord(cacheRec);
}
}
}
-void NewChromSweep::clearCache()
+void NewChromSweep::clearCache(int dbIdx)
{
//delete all objects pointed to by cache
- for (recListIterType iter = _cache.begin(); iter != _cache.end(); iter = _cache.next()) {
- _databaseFRM->deleteRecord(iter->value());
+ recListType &cache = _caches[dbIdx];
+ for (recListIterType iter = cache.begin(); iter != cache.end(); iter = cache.next()) {
+ _dbFRMs[dbIdx]->deleteRecord(iter->value());
}
- _cache.clear();
+ cache.clear();
}
-bool NewChromSweep::chromChange()
+void NewChromSweep::masterScan(RecordKeyVector &retList) {
+ for (int i=0; i < _numDBs; i++) {
+ if (dbFinished(i) || chromChange(i, retList)) {
+ continue;
+ } else {
+
+ // scan the database cache for hits
+ scanCache(i, retList);
+ //skip if we hit the end of the DB
+ // advance the db until we are ahead of the query. update hits and cache as necessary
+ while (_currDbRecs[i] != NULL &&
+ _currQueryRec->sameChrom(_currDbRecs[i]) &&
+ !(_currDbRecs[i]->after(_currQueryRec))) {
+ if (intersects(_currQueryRec, _currDbRecs[i])) {
+ retList.push_back(_currDbRecs[i]);
+ }
+ if (_currQueryRec->after(_currDbRecs[i])) {
+ _dbFRMs[i]->deleteRecord(_currDbRecs[i]);
+ _currDbRecs[i] = NULL;
+ } else {
+ _caches[i].push_back(_currDbRecs[i]);
+ _currDbRecs[i] = NULL;
+ }
+ nextRecord(false, i);
+ }
+ }
+ }
+}
+
+bool NewChromSweep::chromChange(int dbIdx, RecordKeyVector &retList)
{
// the files are on the same chrom
- if (_currDatabaseRec == NULL || _currQueryRec->sameChrom(_currDatabaseRec)) {
+ if (_currDbRecs[dbIdx] == NULL || _currQueryRec->sameChrom(_currDbRecs[dbIdx])) {
return false;
}
// the query is ahead of the database. fast-forward the database to catch-up.
- if (_currQueryRec->chromAfter(_currDatabaseRec)) {
+ if (_currQueryRec->chromAfter(_currDbRecs[dbIdx])) {
- while (_currDatabaseRec != NULL &&
- _currQueryRec->chromAfter(_currDatabaseRec)) {
- _databaseFRM->deleteRecord(_currDatabaseRec);
- nextRecord(false);
+ while (_currDbRecs[dbIdx] != NULL &&
+ _currQueryRec->chromAfter(_currDbRecs[dbIdx])) {
+ _dbFRMs[dbIdx]->deleteRecord(_currDbRecs[dbIdx]);
+ nextRecord(false, dbIdx);
}
- clearCache();
+ clearCache(dbIdx);
return false;
}
// the database is ahead of the query.
else {
// 1. scan the cache for remaining hits on the query's current chrom.
- if (_currQueryRec->getChrName() == _currChromName)
- {
- scanCache();
- }
- // 2. fast-forward until we catch up and report 0 hits until we do.
- else if (_currQueryRec->chromBefore(_currDatabaseRec))
- {
- clearCache();
- }
+ scanCache(dbIdx, retList);
return true;
}
+
+ //control can't reach here, but compiler still wants a return statement.
+ return true;
}
-bool NewChromSweep::next(RecordKeyList &next) {
+bool NewChromSweep::next(RecordKeyVector &retList) {
+ retList.clearVector();
if (_currQueryRec != NULL) {
_queryFRM->deleteRecord(_currQueryRec);
}
- nextRecord(true);
- if (_currQueryRec == NULL) { //eof hit!
- return false;
- }
- if (_currDatabaseRec == NULL && _cache.empty() && !_runToQueryEnd) {
+ if (!nextRecord(true)) return false; // query EOF hit
+
+
+ if (allCurrDBrecsNull() && allCachesEmpty() && !_runToQueryEnd) {
return false;
}
- _hits.clear();
_currChromName = _currQueryRec->getChrName();
- // have we changed chromosomes?
- if (!chromChange()) {
- // scan the database cache for hits
- scanCache();
- //skip if we hit the end of the DB
- // advance the db until we are ahead of the query. update hits and cache as necessary
- while (_currDatabaseRec != NULL &&
- _currQueryRec->sameChrom(_currDatabaseRec) &&
- !(_currDatabaseRec->after(_currQueryRec))) {
- if (intersects(_currQueryRec, _currDatabaseRec)) {
- _hits.push_back(_currDatabaseRec);
- }
- if (_currQueryRec->after(_currDatabaseRec)) {
- _databaseFRM->deleteRecord(_currDatabaseRec);
- _currDatabaseRec = NULL;
- } else {
- _cache.push_back(_currDatabaseRec);
- _currDatabaseRec = NULL;
- }
- nextRecord(false);
- }
+
+ masterScan(retList);
+
+ if (_context->getSortOutput()) {
+ retList.sortVector();
}
- next.setKey(_currQueryRec);
- next.setListNoCopy(_hits);
+
+ retList.setKey(_currQueryRec);
return true;
}
-void NewChromSweep::nextRecord(bool query) {
+bool NewChromSweep::nextRecord(bool query, int dbIdx) {
if (query) {
-// if (!_context->getUseMergedIntervals()) {
- _currQueryRec = _queryFRM->getNextRecord();
-// } else {
-// _currQueryRec = _queryFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
-// }
+ _currQueryRec = _queryFRM->getNextRecord();
if (_currQueryRec != NULL) {
_queryRecordsTotalLength += (unsigned long)(_currQueryRec->getEndPos() - _currQueryRec->getStartPos());
+ return true;
}
+ return false;
} else { //database
-// if (!_context->getUseMergedIntervals()) {
- _currDatabaseRec = _databaseFRM->getNextRecord();
-// } else {
-// _currDatabaseRec = _databaseFRM->allocateAndGetNextMergedRecord(_context->getSameStrand() ? FileRecordMgr::SAME_STRAND_EITHER : FileRecordMgr::ANY_STRAND);
-// }
- if (_currDatabaseRec != NULL) {
- _databaseRecordsTotalLength += (unsigned long)(_currDatabaseRec->getEndPos() - _currDatabaseRec->getStartPos());
+ Record *rec = _dbFRMs[dbIdx]->getNextRecord();
+ _currDbRecs[dbIdx] = rec;
+ if (rec != NULL) {
+ _databaseRecordsTotalLength += (unsigned long)(rec->getEndPos() - rec->getStartPos());
+ return true;
}
+ return false;
}
}
@@ -209,3 +226,29 @@ bool NewChromSweep::intersects(const Record *rec1, const Record *rec2) const
return rec1->sameChromIntersects(rec2, _context->getSameStrand(), _context->getDiffStrand(),
_context->getOverlapFraction(), _context->getReciprocal());
}
+
+
+bool NewChromSweep::allCachesEmpty() {
+ for (int i=0; i < _numDBs; i++) {
+ if (!_caches[i].empty()) {
+ return false;
+ }
+ }
+ return true;
+}
+
+bool NewChromSweep::allCurrDBrecsNull() {
+ for (int i=0; i < _numDBs; i++) {
+ if (_currDbRecs[i] != NULL) {
+ return false;
+ }
+ }
+ return true;
+}
+
+bool NewChromSweep::dbFinished(int dbIdx) {
+ if (_currDbRecs[dbIdx] == NULL && _caches[dbIdx].empty()) {
+ return true;
+ }
+ return false;
+}
diff --git a/src/utils/NewChromsweep/NewChromsweep.h b/src/utils/NewChromsweep/NewChromsweep.h
index 480b399ce0af0fecbf4c7cbe00662ac8d425aafe..1dfe5b7bc543aa14eb42ad2803e943df8fd0862c 100644
--- a/src/utils/NewChromsweep/NewChromsweep.h
+++ b/src/utils/NewChromsweep/NewChromsweep.h
@@ -1,5 +1,5 @@
/*****************************************************************************
- NewChromsweepBed.h
+ NewChromsweep.h
(c) 2009 - Aaron Quinlan
Hall Laboratory
@@ -15,6 +15,7 @@
#include <string>
#include "BTlist.h"
#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
#include <queue>
#include <iostream>
#include <fstream>
@@ -34,61 +35,67 @@ public:
~NewChromSweep(void);
bool init();
- typedef BTlist<const Record *> recListType;
- typedef const BTlistNode<const Record *> * recListIterType;
+ typedef RecordList recListType;
+ typedef const RecordListNode *recListIterType;
// loads next (a pair) with the current query and it's overlaps
- bool next(RecordKeyList &next);
+ bool next(RecordKeyVector &next);
- //MUST call this method after sweep if you want the
- //getTotalRecordLength methods to return the whole length of the
- //record files, rather than just what was used by sweep.
+ // NOTE! You MUST call this method after sweep if you want the
+ // getTotalRecordLength methods to return the whole length of the
+ // record files, rather than just what was used by sweep.
void closeOut();
+
unsigned long getQueryTotalRecordLength() { return _queryRecordsTotalLength; }
unsigned long getDatabaseTotalRecordLength() { return _databaseRecordsTotalLength; }
- // Usage:
- // NewChromSweep sweep = NewChromSweep(queryFileName, databaseFileName);
- // RecordKeyList hits;
- // while (sweep.next(hits))
- // {
- // processHits(hits);
- // }
- // getQueryTotalRecordLength()
- // getDatabaseTotalRecordLength()
-
private:
ContextIntersect *_context;
FileRecordMgr *_queryFRM;
- FileRecordMgr *_databaseFRM;
+ int _numDBs; //don't really need this stored, but here for code brevity.
+ vector<FileRecordMgr *> _dbFRMs;
bool _useMergedIntervals;
unsigned long _queryRecordsTotalLength;
+ vector<unsigned long> _dbFileRecordsLength; //each value in this vector have the
+ //length of all records in the corresponding db file.
+
unsigned long _databaseRecordsTotalLength;
bool _wasInitialized;
// a cache of still active features from the database file
- recListType _cache;
+// typedef enum { BEFORE_QUERY, NEAR_QUERY, AFTER_QUERY, EOF } cacheStatusType;
+// vector <pair<cacheStatusType, recListType> >_caches;
+
+ vector <recListType>_caches;
// the set of hits in the database for the current query
- recListType _hits;
+// recListType _hits;
// the current query and db features.
- Record * _currQueryRec;
- Record *_currDatabaseRec;
+ const Record * _currQueryRec;
+ vector<const Record *> _currDbRecs;
+
// a cache of the current chrom from the query. used to handle chrom changes.
QuickString _currChromName;
bool _runToQueryEnd;
- void nextRecord(bool query); //true fetches next query record, false fetches next db record.
- void nextDatabase();
+ void masterScan(RecordKeyVector &retList);
+
+ bool nextRecord(bool query, int dbIdx = -1); //true fetches next query record, false fetches next db record.
- void scanCache();
- void clearCache();
- bool chromChange();
+ void scanCache(int dbIdx, RecordKeyVector &retList);
+ void clearCache(int dbIdx);
+ bool chromChange(int dbIdx, RecordKeyVector &retList);
+
+ bool dbFinished(int dbIdx);
+
bool intersects(const Record *rec1, const Record *rec2) const;
+ bool allCachesEmpty();
+ bool allCurrDBrecsNull();
+
};
#endif /* NewChromSweep_H */
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
index b7b2f9a456878783864c85b97bcbd3c667c27536..f4d80741c09bab8e7b7d6db455dd59ffcd3307d6 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -75,7 +75,7 @@ void RecordOutputMgr::init(ContextBase *context) {
}
}
-bool RecordOutputMgr::printKeyAndTerminate(RecordKeyList &keyList) {
+bool RecordOutputMgr::printKeyAndTerminate(RecordKeyVector &keyList) {
if (_context->getProgram() == ContextBase::MERGE) {
//when printing merged records, we want to force the printing into
//bed3 format, which is surprisingly difficult to do. Had to use the following:
@@ -95,7 +95,7 @@ bool RecordOutputMgr::printKeyAndTerminate(RecordKeyList &keyList) {
}
-RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyList &keyList, bool bamOutputOnly)
+RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyVector &keyList, bool bamOutputOnly)
{
const Record *record = keyList.getKey();
if (record->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
@@ -118,7 +118,7 @@ RecordOutputMgr::printBamType RecordOutputMgr::printBamRecord(RecordKeyList &key
void RecordOutputMgr::printRecord(const Record *record)
{
- RecordKeyList keyList(record);
+ RecordKeyVector keyList(record);
printRecord(keyList);
}
@@ -137,9 +137,9 @@ void RecordOutputMgr::printRecord(const Record *record, const QuickString & valu
}
}
-void RecordOutputMgr::printRecord(RecordKeyList &keyList) {
+void RecordOutputMgr::printRecord(RecordKeyVector &keyList) {
if (keyList.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
- RecordKeyList blockList(keyList.getKey());
+ RecordKeyVector blockList(keyList.getKey());
bool deleteBlocks = false;
_bamBlockMgr->getBlocks(blockList, deleteBlocks);
printRecord(keyList, &blockList);
@@ -152,7 +152,7 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList) {
}
-void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockList)
+void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blockList)
{
if (needsFlush()) {
flush();
@@ -198,8 +198,8 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
return;
}
int hitIdx = 0;
- for (RecordKeyList::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
- reportOverlapDetail(keyList.getKey(), iter->value(), hitIdx);
+ for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
+ reportOverlapDetail(keyList.getKey(), *iter, hitIdx);
hitIdx++;
}
}
@@ -306,6 +306,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
(static_cast<ContextIntersect *>(_context))->getWriteB()) || (static_cast<ContextIntersect *>(_context))->getLeftJoin()) {
printKey(keyRecord);
tab();
+ addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
newline();
if (needsFlush()) flush();
@@ -318,6 +319,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
else if ((static_cast<ContextIntersect *>(_context))->getWriteB()) {
printKey(keyRecord, *startStr, *endStr);
tab();
+ addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
newline();
if (needsFlush()) flush();
@@ -331,6 +333,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
}
printKey(keyRecord);
tab();
+ addDbFileId(hitRecord->getFileIdx());
hitRecord->print(_outBuf);
tab();
int2str(printOverlapBases, _outBuf, true);
@@ -339,7 +342,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
}
}
-void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
+void RecordOutputMgr::reportOverlapSummary(RecordKeyVector &keyList)
{
int numOverlapsFound = (int)keyList.size();
if ((static_cast<ContextIntersect *>(_context))->getAnyHit() && numOverlapsFound > 0) {
@@ -365,6 +368,17 @@ void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
}
}
+void RecordOutputMgr::addDbFileId(int fileId) {
+ if ((static_cast<ContextIntersect *>(_context))->getNumDatabaseFiles() == 1) return;
+ if (!_context->getUseDBnameTags() && (!_context->getUseDBfileNames())) {
+ _outBuf.append(fileId);
+ } else if (_context->getUseDBnameTags()){
+ _outBuf.append((static_cast<ContextIntersect *>(_context))->getDatabaseNameTag((static_cast<ContextIntersect *>(_context))->getDbIdx(fileId)));
+ } else {
+ _outBuf.append(_context->getInputFileName(fileId));
+ }
+ tab();
+}
void RecordOutputMgr::null(bool queryType, bool dbType)
{
@@ -373,7 +387,7 @@ void RecordOutputMgr::null(bool queryType, bool dbType)
if (queryType) {
recordType = (static_cast<ContextIntersect *>(_context))->getQueryRecordType();
} else if (dbType) {
- recordType = (static_cast<ContextIntersect *>(_context))->getDatabaseRecordType();
+ recordType = (static_cast<ContextIntersect *>(_context))->getDatabaseRecordType(0);
}
} else {
recordType = _context->getFile(0)->getRecordType();
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.h b/src/utils/RecordOutputMgr/RecordOutputMgr.h
index 1a7fe609835e2e87fcbbf0e13e662362430e68d7..33ad8a11bcff7920f67601a00dffd9b07fafa509 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.h
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.h
@@ -9,7 +9,7 @@
#define RECORDOUTPUTMGR_H_
#include "ContextBase.h"
-#include "RecordKeyList.h"
+#include "RecordKeyVector.h"
#include "api/BamWriter.h"
class BlockMgr;
@@ -23,7 +23,7 @@ public:
void init(ContextBase *context);
void printRecord(const Record *record);
- void printRecord(RecordKeyList &keyList);
+ void printRecord(RecordKeyVector &keyList);
void printRecord(const Record *record, const QuickString & value);
//where necessary, pass additional information about splits through the blockMgr.
@@ -35,7 +35,7 @@ private:
ContextBase *_context;
bool _printable;
BamTools::BamWriter *_bamWriter;
- RecordKeyList *_currBamBlockList;
+ RecordKeyVector *_currBamBlockList;
QuickString _outBuf;
@@ -48,14 +48,15 @@ private:
void newline() { _outBuf.append('\n'); }
void null(bool queryType, bool dbType);
- void printRecord(RecordKeyList &keyList, RecordKeyList *blockList);
+ void printRecord(RecordKeyVector &keyList, RecordKeyVector *blockList);
void printKey(const Record *key);
void printKey(const Record *key, const QuickString & start, const QuickString & end);
- bool printKeyAndTerminate(RecordKeyList &keyList);
- printBamType printBamRecord(RecordKeyList &keyList, bool bamOutputOnly = false);
+ void addDbFileId(int fileId);
+ bool printKeyAndTerminate(RecordKeyVector &keyList);
+ printBamType printBamRecord(RecordKeyVector &keyList, bool bamOutputOnly = false);
void checkForHeader();
void reportOverlapDetail(const Record *keyRecord, const Record *hitRecord, int hitIdx = 0);
- void reportOverlapSummary(RecordKeyList &keyList);
+ void reportOverlapSummary(RecordKeyVector &keyList);
static const unsigned int MAX_OUTBUF_SIZE = 16384; //16 K
diff --git a/src/utils/general/CommonHelp.cpp b/src/utils/general/CommonHelp.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a0efc473dc915ca64667e415e7245675f5082817
--- /dev/null
+++ b/src/utils/general/CommonHelp.cpp
@@ -0,0 +1,17 @@
+/*
+ * CommonHelp.cpp
+ *
+ * Created on: Jul 2, 2014
+ * Author: nek3d
+ */
+#include "CommonHelp.h"
+
+void CommonHelp() {
+ cerr << "\t-iobuf\t" << "Follow with desired integer size of read buffer." << endl;
+ cerr << "\t\t" << "Optional suffixes K/M/G supported." << endl;
+ cerr << "\t\t" << "Note: currently has no effect with compressed files." << endl << endl;
+}
+
+
+
+
diff --git a/src/utils/general/CommonHelp.h b/src/utils/general/CommonHelp.h
new file mode 100644
index 0000000000000000000000000000000000000000..c54c4556509a2d07be6abdd695fa6225bf75e742
--- /dev/null
+++ b/src/utils/general/CommonHelp.h
@@ -0,0 +1,19 @@
+/*
+ * CommonHelpFile.h
+ *
+ * Created on: Jul 2, 2014
+ * Author: nek3d
+ */
+
+#ifndef COMMONHELPFILE_H_
+#define COMMONHELPFILE_H_
+
+using namespace std;
+
+#include <iostream>
+
+extern void CommonHelp();
+
+
+
+#endif /* COMMONHELPFILE_H_ */
diff --git a/src/utils/general/Makefile b/src/utils/general/Makefile
index 20d7aeead018248fc8d954d4eb982c66c4009701..33f94ecef59b113dca056a1c9bbfdda3bfe793e9 100644
--- a/src/utils/general/Makefile
+++ b/src/utils/general/Makefile
@@ -9,8 +9,9 @@ INCLUDES = -I$(UTILITIES_DIR)/lineFileUtilities/
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= QuickString.h QuickString.cpp ParseTools.h ParseTools.cpp PushBackStreamBuf.cpp PushBackStreamBuf.h CompressionTools.h CompressionTools.cpp Tokenizer.h Tokenizer.h
-OBJECTS= QuickString.o ParseTools.o PushBackStreamBuf.o CompressionTools.o Tokenizer.o
+SOURCES= QuickString.h QuickString.cpp ParseTools.h ParseTools.cpp PushBackStreamBuf.cpp PushBackStreamBuf.h CompressionTools.h CompressionTools.cpp \
+ Tokenizer.h Tokenizer.h CommonHelp.h CommonHelp.cpp
+OBJECTS= QuickString.o ParseTools.o PushBackStreamBuf.o CompressionTools.o Tokenizer.o CommonHelp.o
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
all: $(BUILT_OBJECTS)
@@ -23,6 +24,6 @@ $(BUILT_OBJECTS): $(SOURCES)
clean:
@echo "Cleaning up."
- @rm -f $(OBJ_DIR)/QuickString.o $(OBJ_DIR)/ParseTools.o $(OBJ_DIR)/PushBackStreamBuf.o $(OBJ_DIR)/Tokenizer.o
+ @rm -f $(OBJ_DIR)/QuickString.o $(OBJ_DIR)/ParseTools.o $(OBJ_DIR)/PushBackStreamBuf.o $(OBJ_DIR)/Tokenizer.o $(OBJ_DIR)/CommonHelp.o
.PHONY: clean
diff --git a/src/utils/general/PushBackStreamBuf.h b/src/utils/general/PushBackStreamBuf.h
index d2538eaa3209ef77477bbdd8ffd8f63606806401..1b2e2301e16f933fc5df95c643ea5c6ef9a15d22 100644
--- a/src/utils/general/PushBackStreamBuf.h
+++ b/src/utils/general/PushBackStreamBuf.h
@@ -31,8 +31,6 @@ protected:
private:
streambuf* _primary_stream;
BTlist<int> _buffer;
- static const int SCAN_BUFFER_SIZE = 8192; //8 KB buffer
- static const int MAIN_BUFFER_SIZE = 128 * 1024; //128K buffer
};
diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
index 9e061866f62969778b829c247bad8d32345aad58..5f536156914546e08ea3dfdcddef46ddcb89bd3b 100644
--- a/src/utils/general/QuickString.cpp
+++ b/src/utils/general/QuickString.cpp
@@ -67,6 +67,11 @@ void QuickString::clear() {
_currSize = 0;
}
+void QuickString::release() {
+ free(_buffer);
+ _currCapacity = DEFAULT_CAPACITY;
+ build();
+}
QuickString &QuickString::operator = (const char *inBuf){
set(inBuf, strlen(inBuf));
diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
index 1024a25f4449149bf19a68c23112228ec8e72a89..93f34bbc52bc24001e8182455cccb0794c970b0d 100644
--- a/src/utils/general/QuickString.h
+++ b/src/utils/general/QuickString.h
@@ -31,6 +31,7 @@ public:
bool empty() const { return _currSize == 0; }
void clear(); //only clears buffer, doesn't delete it.
+ void release(); //will deallocate current buffer, reallocate it at default size.
QuickString &operator = (const string &);
QuickString &operator = (const char *);
QuickString &operator = (const QuickString &);
diff --git a/test/intersect/multi_intersect/d1.bed b/test/intersect/multi_intersect/d1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..91a43d13300eb670f065b5b31097f8c3019951d0
--- /dev/null
+++ b/test/intersect/multi_intersect/d1.bed
@@ -0,0 +1,9 @@
+chr1 5 25
+chr1 65 75
+chr1 95 100
+chr2 5 25
+chr2 65 75
+chr2 95 100
+chr3 5 25
+chr3 65 75
+chr3 95 100
diff --git a/test/intersect/multi_intersect/d2.bed b/test/intersect/multi_intersect/d2.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c2b4e526c3278797ef2bfd4fb85625ac452e1128
--- /dev/null
+++ b/test/intersect/multi_intersect/d2.bed
@@ -0,0 +1,6 @@
+chr1 40 50
+chr1 110 125
+chr2 40 50
+chr2 110 125
+chr3 40 50
+chr3 110 125
diff --git a/test/intersect/multi_intersect/d3.bed b/test/intersect/multi_intersect/d3.bed
new file mode 100644
index 0000000000000000000000000000000000000000..46862402f8e7f825026125905fb9653389c976ff
--- /dev/null
+++ b/test/intersect/multi_intersect/d3.bed
@@ -0,0 +1,3 @@
+chr1 85 115
+chr2 85 115
+chr3 85 115
diff --git a/test/intersect/multi_intersect/d4.bed b/test/intersect/multi_intersect/d4.bed
new file mode 100644
index 0000000000000000000000000000000000000000..34f4e61afba204358755a9382c3ebc7ac3cd111c
--- /dev/null
+++ b/test/intersect/multi_intersect/d4.bed
@@ -0,0 +1,9 @@
+chr1 5 25
+chr1 65 75
+chr1 95 100
+chr2 5 25
+chr2 65 75
+chr2 95 100
+chr10 5 25
+chr10 65 75
+chr10 95 100
diff --git a/test/intersect/multi_intersect/d5.bed b/test/intersect/multi_intersect/d5.bed
new file mode 100644
index 0000000000000000000000000000000000000000..8f03c32596c3ccd083e56e933783ca706196e41f
--- /dev/null
+++ b/test/intersect/multi_intersect/d5.bed
@@ -0,0 +1,6 @@
+chr1 40 50
+chr1 110 125
+chr2 40 50
+chr2 110 125
+chr10 40 50
+chr10 110 125
diff --git a/test/intersect/multi_intersect/d6.bed b/test/intersect/multi_intersect/d6.bed
new file mode 100644
index 0000000000000000000000000000000000000000..e1026a74057e9daa78ddf979b963d1cb0c2a8485
--- /dev/null
+++ b/test/intersect/multi_intersect/d6.bed
@@ -0,0 +1,3 @@
+chr1 85 115
+chr2 85 115
+chr10 85 115
diff --git a/test/intersect/multi_intersect/d7.bed b/test/intersect/multi_intersect/d7.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c1220eb3d63ba894fe7d3ef30861de340688bc9c
--- /dev/null
+++ b/test/intersect/multi_intersect/d7.bed
@@ -0,0 +1,10 @@
+# DB 7 Header line.
+chr1 5 25 d7_1 100 +
+chr1 65 75 d7_2 100 -
+chr1 95 100 d7_3 100 +
+chr2 5 25 d7_4 100 -
+chr2 65 75 d7_5 100 .
+chr2 95 100 d7_6 100 -
+chr3 5 25 d7_7 100 +
+chr3 65 75 d7_8 100 -
+chr3 95 100 d7_9 100 .
diff --git a/test/intersect/multi_intersect/d8.bed b/test/intersect/multi_intersect/d8.bed
new file mode 100644
index 0000000000000000000000000000000000000000..565eb9808623e2c636a1b8905a6077b7f9d70cb1
--- /dev/null
+++ b/test/intersect/multi_intersect/d8.bed
@@ -0,0 +1,7 @@
+# DB 8 Header Line.
+chr1 40 50 d8_1 100 -
+chr1 110 125 d8_2 100 +
+chr2 40 50 d8_3 100 -
+chr2 110 125 d8_4 100 .
+chr3 40 50 d8_5 100 -
+chr3 110 125 d8_6 100 +
diff --git a/test/intersect/multi_intersect/d9.bed b/test/intersect/multi_intersect/d9.bed
new file mode 100644
index 0000000000000000000000000000000000000000..188c7b4894a1cc4b0e068c2c50525ecb335a429f
--- /dev/null
+++ b/test/intersect/multi_intersect/d9.bed
@@ -0,0 +1,4 @@
+# DB 9 Header Line.
+chr1 85 115 d9_1 100 +
+chr2 85 115 d9_1 100 -
+chr3 85 115 d9_1 100 +
diff --git a/test/intersect/multi_intersect/g.bed b/test/intersect/multi_intersect/g.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c340e1413e15f4f8d94159d24e4bf29aded418d3
--- /dev/null
+++ b/test/intersect/multi_intersect/g.bed
@@ -0,0 +1,3 @@
+chr1 200
+chr2 200
+chr10 200
diff --git a/test/intersect/multi_intersect/query.bed b/test/intersect/multi_intersect/query.bed
new file mode 100644
index 0000000000000000000000000000000000000000..b778252d69bb06b4345b309041303f84818c23fc
--- /dev/null
+++ b/test/intersect/multi_intersect/query.bed
@@ -0,0 +1,12 @@
+chr1 1 20
+chr1 40 45
+chr1 70 90
+chr1 105 120
+chr2 1 20
+chr2 40 45
+chr2 70 90
+chr2 105 120
+chr3 1 20
+chr3 40 45
+chr3 70 90
+chr3 105 120
diff --git a/test/intersect/multi_intersect/query2.bed b/test/intersect/multi_intersect/query2.bed
new file mode 100644
index 0000000000000000000000000000000000000000..dd6000e6666c58be5442b54cdc0f1cfe7dfad1a4
--- /dev/null
+++ b/test/intersect/multi_intersect/query2.bed
@@ -0,0 +1,13 @@
+# Query 2 Header Line.
+chr1 1 20
+chr1 40 45
+chr1 70 90
+chr1 105 120
+chr2 1 20
+chr2 40 45
+chr2 70 90
+chr2 105 120
+chr10 1 20
+chr10 40 45
+chr10 70 90
+chr10 105 120
diff --git a/test/intersect/multi_intersect/query3.bed b/test/intersect/multi_intersect/query3.bed
new file mode 100644
index 0000000000000000000000000000000000000000..0c875c8bb2162d069efc891b15f42fd66657b955
--- /dev/null
+++ b/test/intersect/multi_intersect/query3.bed
@@ -0,0 +1,13 @@
+# Query 3 Header Line.
+chr1 1 20 q1 100 +
+chr1 40 45 q2 100 +
+chr1 70 90 q3 100 +
+chr1 105 120 q4 100 +
+chr2 1 20 q5 100 +
+chr2 40 45 q6 100 +
+chr2 70 90 q7 100 +
+chr2 105 120 q8 100 +
+chr3 1 20 q9 100 +
+chr3 40 45 q10 100 +
+chr3 70 90 q11 100 +
+chr3 105 120 q12 100 +
diff --git a/test/intersect/multi_intersect/test-multi_intersect.sh b/test/intersect/multi_intersect/test-multi_intersect.sh
new file mode 100644
index 0000000000000000000000000000000000000000..ed3b4ae80b44e3fc833d372e7f583361b634e8f6
--- /dev/null
+++ b/test/intersect/multi_intersect/test-multi_intersect.sh
@@ -0,0 +1,404 @@
+echo -e \
+"\n###########################################################
+#
+# MULTIPLE DATABASE INTERSECTION
+#
+###########################################################\n"
+
+
+BT=${BT-../../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+# Test the intersection of a query with 3 dbs against
+# the merged and sorted result of 3
+# seperate intersections of the query with each db.
+#
+# First make sure the 3 seperate intersections are correct.
+#
+############################################################
+echo " intersect.t01...\c"
+echo \
+"chr1 5 20
+chr1 70 75
+chr2 5 20
+chr2 70 75
+chr3 5 20
+chr3 70 75" > exp1
+$BT intersect -a query.bed -b d1.bed > obs
+check obs exp1
+rm obs
+
+echo " intersect.t02...\c"
+echo \
+"chr1 40 45
+chr1 110 120
+chr2 40 45
+chr2 110 120
+chr3 40 45
+chr3 110 120" > exp2
+$BT intersect -a query.bed -b d2.bed > obs
+check obs exp2
+rm obs
+
+echo " intersect.t03...\c"
+echo \
+"chr1 85 90
+chr1 105 115
+chr2 85 90
+chr2 105 115
+chr3 85 90
+chr3 105 115" > exp3
+$BT intersect -a query.bed -b d3.bed > obs
+check obs exp3
+rm obs
+
+###########################################################
+# Now test that the R-tree (unsorted input) with sorted
+# output will give the correct result
+###########################################################
+echo " intersect.t04...\c"
+cat exp1 exp2 exp3 | sort -k1,1 -k2,2n > exp
+$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -sortout > obs
+check exp obs
+rm obs exp1 exp2 exp3
+
+
+###########################################################
+# And then test that sorted input with sorted
+# output will give the correct result
+###########################################################
+echo " intersect.t05...\c"
+$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -sorted -sortout > obs
+check exp obs
+rm obs exp
+
+
+###########################################################
+#
+# Now repeat the above with chroms in a non-standard order
+#
+###########################################################
+
+echo " intersect.t06...\c"
+echo \
+"chr1 5 20
+chr1 70 75
+chr2 5 20
+chr2 70 75
+chr10 5 20
+chr10 70 75" > exp1
+$BT intersect -a query2.bed -b d4.bed > obs
+check obs exp1
+rm obs
+
+echo " intersect.t07...\c"
+echo \
+"chr1 40 45
+chr1 110 120
+chr2 40 45
+chr2 110 120
+chr10 40 45
+chr10 110 120" > exp2
+$BT intersect -a query2.bed -b d5.bed > obs
+check obs exp2
+rm obs
+
+echo " intersect.t08...\c"
+echo \
+"chr1 85 90
+chr1 105 115
+chr2 85 90
+chr2 105 115
+chr10 85 90
+chr10 105 115" > exp3
+$BT intersect -a query2.bed -b d6.bed > obs
+check obs exp3
+rm obs
+
+###########################################################
+# Now test that the R-tree (unsorted input) with sorted
+# output will give the correct result
+###########################################################
+echo " intersect.t09...\c"
+cat exp1 exp2 exp3 | sort -k1,1V -k2,2n > exp
+$BT intersect -a query2.bed -b d4.bed d5.bed d6.bed -g g.bed -sortout > obs
+check exp obs
+rm obs exp1 exp2 exp3
+
+
+###########################################################
+# And then test that sorted input with sorted
+# output will give the correct result
+###########################################################
+echo " intersect.t10...\c"
+$BT intersect -a query2.bed -b d4.bed d5.bed d6.bed -sorted -g g.bed -sortout > obs
+check exp obs
+rm obs exp
+
+
+
+###########################################################
+#
+# TEST VARIOUS CMD LINE OUTPUT OPTIONS
+#
+###########################################################
+
+
+###########################################################
+# Test -c option
+###########################################################
+echo " intersect.t11...\c"
+echo \
+"chr1 1 20 1
+chr1 40 45 1
+chr1 70 90 2
+chr1 105 120 2
+chr2 1 20 1
+chr2 40 45 1
+chr2 70 90 2
+chr2 105 120 2
+chr3 1 20 1
+chr3 40 45 1
+chr3 70 90 2
+chr3 105 120 2" > exp
+$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -c -sorted -sortout > obs
+check exp obs
+rm exp obs
+
+
+###########################################################
+# Test -f option
+###########################################################
+echo " intersect.t12...\c"
+echo \
+"chr1 5 20
+chr1 40 45
+chr1 110 120
+chr1 105 115
+chr2 5 20
+chr2 40 45
+chr2 110 120
+chr2 105 115
+chr3 5 20
+chr3 40 45
+chr3 110 120
+chr3 105 115" > exp
+$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -f .6 > obs
+check exp obs
+
+
+###########################################################
+# Test -s option
+###########################################################
+echo " intersect.t13...\c"
+echo \
+"chr1 5 20 q1 100 +
+chr1 85 90 q3 100 +
+chr1 110 120 q4 100 +
+chr1 105 115 q4 100 +
+chr3 5 20 q9 100 +
+chr3 85 90 q11 100 +
+chr3 110 120 q12 100 +
+chr3 105 115 q12 100 +" > exp
+$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -s > obs
+check exp obs
+rm exp obs
+
+
+###########################################################
+# Test -s option
+###########################################################
+echo " intersect.t13...\c"
+echo \
+"chr1 40 45 q2 100 +
+chr1 70 75 q3 100 +
+chr2 5 20 q5 100 +
+chr2 40 45 q6 100 +
+chr2 85 90 q7 100 +
+chr2 105 115 q8 100 +
+chr3 40 45 q10 100 +
+chr3 70 75 q11 100 +" > exp
+$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -S > obs
+check exp obs
+rm exp obs
+
+
+###########################################################
+# Test -wo option
+###########################################################
+echo " intersect.t14...\c"
+echo \
+"chr1 1 20 1 chr1 5 25 15
+chr1 40 45 2 chr1 40 50 5
+chr1 70 90 1 chr1 65 75 5
+chr1 70 90 3 chr1 85 115 5
+chr1 105 120 2 chr1 110 125 10
+chr1 105 120 3 chr1 85 115 10
+chr2 1 20 1 chr2 5 25 15
+chr2 40 45 2 chr2 40 50 5
+chr2 70 90 1 chr2 65 75 5
+chr2 70 90 3 chr2 85 115 5
+chr2 105 120 2 chr2 110 125 10
+chr2 105 120 3 chr2 85 115 10
+chr3 1 20 1 chr3 5 25 15
+chr3 40 45 2 chr3 40 50 5
+chr3 70 90 1 chr3 65 75 5
+chr3 70 90 3 chr3 85 115 5
+chr3 105 120 2 chr3 110 125 10
+chr3 105 120 3 chr3 85 115 10" > exp
+$BT intersect -a query.bed -b d1.bed d2.bed d3.bed -wo > obs
+check exp obs
+rm exp obs
+
+
+
+###########################################################
+# Test -wa -wb -header option
+###########################################################
+echo " intersect.t15...\c"
+echo \
+"# Query 3 Header Line.
+chr1 1 20 q1 100 + 1 chr1 5 25 d7_1 100 +
+chr1 40 45 q2 100 + 2 chr1 40 50 d8_1 100 -
+chr1 70 90 q3 100 + 1 chr1 65 75 d7_2 100 -
+chr1 70 90 q3 100 + 3 chr1 85 115 d9_1 100 +
+chr1 105 120 q4 100 + 2 chr1 110 125 d8_2 100 +
+chr1 105 120 q4 100 + 3 chr1 85 115 d9_1 100 +
+chr2 1 20 q5 100 + 1 chr2 5 25 d7_4 100 -
+chr2 40 45 q6 100 + 2 chr2 40 50 d8_3 100 -
+chr2 70 90 q7 100 + 1 chr2 65 75 d7_5 100 .
+chr2 70 90 q7 100 + 3 chr2 85 115 d9_1 100 -
+chr2 105 120 q8 100 + 2 chr2 110 125 d8_4 100 .
+chr2 105 120 q8 100 + 3 chr2 85 115 d9_1 100 -
+chr3 1 20 q9 100 + 1 chr3 5 25 d7_7 100 +
+chr3 40 45 q10 100 + 2 chr3 40 50 d8_5 100 -
+chr3 70 90 q11 100 + 1 chr3 65 75 d7_8 100 -
+chr3 70 90 q11 100 + 3 chr3 85 115 d9_1 100 +
+chr3 105 120 q12 100 + 2 chr3 110 125 d8_6 100 +
+chr3 105 120 q12 100 + 3 chr3 85 115 d9_1 100 +" > exp
+$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -wa -wb -header > obs
+check exp obs
+rm exp obs
+
+
+
+###########################################################
+# Test the -filenames option, before db listing
+###########################################################
+echo " intersect.t16...\c"
+echo \
+"chr1 1 20 q1 100 + d7.bed chr1 5 25 d7_1 100 +
+chr1 40 45 q2 100 + d8.bed chr1 40 50 d8_1 100 -
+chr1 70 90 q3 100 + d7.bed chr1 65 75 d7_2 100 -
+chr1 70 90 q3 100 + d9.bed chr1 85 115 d9_1 100 +
+chr1 105 120 q4 100 + d8.bed chr1 110 125 d8_2 100 +
+chr1 105 120 q4 100 + d9.bed chr1 85 115 d9_1 100 +
+chr2 1 20 q5 100 + d7.bed chr2 5 25 d7_4 100 -
+chr2 40 45 q6 100 + d8.bed chr2 40 50 d8_3 100 -
+chr2 70 90 q7 100 + d7.bed chr2 65 75 d7_5 100 .
+chr2 70 90 q7 100 + d9.bed chr2 85 115 d9_1 100 -
+chr2 105 120 q8 100 + d8.bed chr2 110 125 d8_4 100 .
+chr2 105 120 q8 100 + d9.bed chr2 85 115 d9_1 100 -
+chr3 1 20 q9 100 + d7.bed chr3 5 25 d7_7 100 +
+chr3 40 45 q10 100 + d8.bed chr3 40 50 d8_5 100 -
+chr3 70 90 q11 100 + d7.bed chr3 65 75 d7_8 100 -
+chr3 70 90 q11 100 + d9.bed chr3 85 115 d9_1 100 +
+chr3 105 120 q12 100 + d8.bed chr3 110 125 d8_6 100 +
+chr3 105 120 q12 100 + d9.bed chr3 85 115 d9_1 100 +" > exp
+$BT intersect -a query3.bed -filenames -b d7.bed d8.bed d9.bed -wa -wb > obs
+check exp obs
+rm exp obs
+
+###########################################################
+# Test the -filenames option, after db listing
+###########################################################
+echo " intersect.t17...\c"
+echo \
+"chr1 1 20 q1 100 + d7.bed chr1 5 25 d7_1 100 +
+chr1 40 45 q2 100 + d8.bed chr1 40 50 d8_1 100 -
+chr1 70 90 q3 100 + d7.bed chr1 65 75 d7_2 100 -
+chr1 70 90 q3 100 + d9.bed chr1 85 115 d9_1 100 +
+chr1 105 120 q4 100 + d8.bed chr1 110 125 d8_2 100 +
+chr1 105 120 q4 100 + d9.bed chr1 85 115 d9_1 100 +
+chr2 1 20 q5 100 + d7.bed chr2 5 25 d7_4 100 -
+chr2 40 45 q6 100 + d8.bed chr2 40 50 d8_3 100 -
+chr2 70 90 q7 100 + d7.bed chr2 65 75 d7_5 100 .
+chr2 70 90 q7 100 + d9.bed chr2 85 115 d9_1 100 -
+chr2 105 120 q8 100 + d8.bed chr2 110 125 d8_4 100 .
+chr2 105 120 q8 100 + d9.bed chr2 85 115 d9_1 100 -
+chr3 1 20 q9 100 + d7.bed chr3 5 25 d7_7 100 +
+chr3 40 45 q10 100 + d8.bed chr3 40 50 d8_5 100 -
+chr3 70 90 q11 100 + d7.bed chr3 65 75 d7_8 100 -
+chr3 70 90 q11 100 + d9.bed chr3 85 115 d9_1 100 +
+chr3 105 120 q12 100 + d8.bed chr3 110 125 d8_6 100 +
+chr3 105 120 q12 100 + d9.bed chr3 85 115 d9_1 100 +" > exp
+$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -filenames -wa -wb > obs
+check exp obs
+rm exp obs
+
+
+###########################################################
+# Test the -names option, before db listing
+###########################################################
+echo " intersect.t18...\c"
+echo \
+"chr1 1 20 q1 100 + blue chr1 5 25 d7_1 100 +
+chr1 40 45 q2 100 + red chr1 40 50 d8_1 100 -
+chr1 70 90 q3 100 + blue chr1 65 75 d7_2 100 -
+chr1 70 90 q3 100 + green chr1 85 115 d9_1 100 +
+chr1 105 120 q4 100 + red chr1 110 125 d8_2 100 +
+chr1 105 120 q4 100 + green chr1 85 115 d9_1 100 +
+chr2 1 20 q5 100 + blue chr2 5 25 d7_4 100 -
+chr2 40 45 q6 100 + red chr2 40 50 d8_3 100 -
+chr2 70 90 q7 100 + blue chr2 65 75 d7_5 100 .
+chr2 70 90 q7 100 + green chr2 85 115 d9_1 100 -
+chr2 105 120 q8 100 + red chr2 110 125 d8_4 100 .
+chr2 105 120 q8 100 + green chr2 85 115 d9_1 100 -
+chr3 1 20 q9 100 + blue chr3 5 25 d7_7 100 +
+chr3 40 45 q10 100 + red chr3 40 50 d8_5 100 -
+chr3 70 90 q11 100 + blue chr3 65 75 d7_8 100 -
+chr3 70 90 q11 100 + green chr3 85 115 d9_1 100 +
+chr3 105 120 q12 100 + red chr3 110 125 d8_6 100 +
+chr3 105 120 q12 100 + green chr3 85 115 d9_1 100 +" > exp
+$BT intersect -a query3.bed -names blue red green -b d7.bed d8.bed d9.bed -wa -wb > obs
+check exp obs
+rm exp obs
+
+###########################################################
+# Test the -names option, after db listing
+###########################################################
+echo " intersect.t19...\c"
+echo \
+"chr1 1 20 q1 100 + blue chr1 5 25 d7_1 100 +
+chr1 40 45 q2 100 + red chr1 40 50 d8_1 100 -
+chr1 70 90 q3 100 + blue chr1 65 75 d7_2 100 -
+chr1 70 90 q3 100 + green chr1 85 115 d9_1 100 +
+chr1 105 120 q4 100 + red chr1 110 125 d8_2 100 +
+chr1 105 120 q4 100 + green chr1 85 115 d9_1 100 +
+chr2 1 20 q5 100 + blue chr2 5 25 d7_4 100 -
+chr2 40 45 q6 100 + red chr2 40 50 d8_3 100 -
+chr2 70 90 q7 100 + blue chr2 65 75 d7_5 100 .
+chr2 70 90 q7 100 + green chr2 85 115 d9_1 100 -
+chr2 105 120 q8 100 + red chr2 110 125 d8_4 100 .
+chr2 105 120 q8 100 + green chr2 85 115 d9_1 100 -
+chr3 1 20 q9 100 + blue chr3 5 25 d7_7 100 +
+chr3 40 45 q10 100 + red chr3 40 50 d8_5 100 -
+chr3 70 90 q11 100 + blue chr3 65 75 d7_8 100 -
+chr3 70 90 q11 100 + green chr3 85 115 d9_1 100 +
+chr3 105 120 q12 100 + red chr3 110 125 d8_6 100 +
+chr3 105 120 q12 100 + green chr3 85 115 d9_1 100 +" > exp
+$BT intersect -a query3.bed -b d7.bed d8.bed d9.bed -names blue red green -wa -wb > obs
+check exp obs
+rm exp obs
+
+
+
diff --git a/test/intersect/new_test-intersect.sh~ b/test/intersect/new_test-intersect.sh~
new file mode 100755
index 0000000000000000000000000000000000000000..55b01ed54d89aeedd7bdb34a4563011a9fd18321
--- /dev/null
+++ b/test/intersect/new_test-intersect.sh~
@@ -0,0 +1,766 @@
+BT=${BT-../../bin/bedtools}
+
+check()
+{
+ if diff $1 $2; then
+ echo ok
+ else
+ echo fail
+ fi
+}
+
+###########################################################
+# Test intersection of a as bed from file vs b as bed from file
+############################################################
+echo " intersect.new.t01...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a.bed -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t02...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t03...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a.bed | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bed from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t04...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a.bed) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t05...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_gzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t06...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_gzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t07...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_gzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as gzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t08...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_gzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t09...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_bgzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t10...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_bgzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t11...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_bgzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bgzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t12...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_bgzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a as bam from file vs b as bed from file
+############################################################
+echo " intersect.new.t13...\c"
+$BT intersect -a a.bam -b b.bed> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t14...\c"
+$BT intersect -a - -b b.bed < a.bam> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t15...\c"
+cat a.bam | $BT intersect -a - -b b.bed> obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of a as bam from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t16...\c"
+$BT intersect -a <(cat a.bam) -b b.bed > obs
+check obs aVSb.bam
+rm obs
+
+
+###########################################################
+# Test intersection of bam file containing both good reads
+# and those where both read and mate are unmapped vs b file
+# as bed.
+############################################################
+echo " intersect.new.t17...\c"
+echo \
+"chr1 100 101 a2 255 - 100 200 0,0,0 1 100, 0,
+chr1 100 110 a2 255 - 100 200 0,0,0 1 100, 0," > exp
+$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of bam file containing both good reads
+# and those where both read and mate are unmapped vs b file
+# as bed, with noHit (-v) option.
+############################################################
+echo " intersect.new.t18...\c"
+echo \
+"chr1 10 20 a1 255 + 10 20 0,0,0 1 10, 0,
+. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:5780:51632#/2 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1101:8137:99409#/2 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/1 0 . -1 -1 -1 0,0,0 0 . .
+. -1 -1 FCC1MK2ACXX:1:1102:6799:2633#/2 0 . -1 -1 -1 0,0,0 0 . ." > exp
+$BT intersect -a a_with_bothUnmapped.bam -b b.bed -bed -v > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of bam file containing read where query
+# is mapped and mate is not.
+############################################################
+echo " intersect.new.t19...\c"
+echo \
+"chr1 98650 98704 FCC1MK2ACXX:1:1212:13841:9775#/1 0 + 98604 98704 0,0,0 1 100, 0," > exp
+$BT intersect -a oneUnmapped.bam -b j1.bed -bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test intersection of bam file containing read where query
+# is mapped and mate is not, with noHit (-v) option.
+############################################################
+echo " intersect.new.t20...\c"
+echo \
+"chr1 -1 -1 FCC1MK2ACXX:1:1212:13841:9775#/2 0 . -1 -1 -1 0,0,0 0 . ." > exp
+$BT intersect -a oneUnmapped.bam -b j1.bed -bed -v > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of bam file containing read where query
+# is unmapped but mate is mapped.
+############################################################
+echo " intersect.new.t20.b...\c"
+touch exp
+$BT intersect -a queryUnmappedMateMappedCoordsInvalid.bam -b j1.bed -bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test intersection of bam file containing read where one
+# mate is mapped and one is not, with noHit (-v) option.
+############################################################
+echo " intersect.new.t20.c...\c"
+echo ". -1 -1 TTTACCTTT:4FSQ5P1:286:D2GA7ACXX:6:2316:20858:89646 0 . -1 -1 -1 0,0,0 0 . ." > exp
+$BT intersect -a queryUnmappedMateMappedCoordsInvalid.bam -b j1.bed -bed -v > obs
+check obs exp
+rm obs exp
+
+
+
+
+
+###########################################################
+# Test intersection with -sorted, see that order specified
+# in genome file is enforced.
+############################################################
+echo " intersect.new.t21...\c"
+echo \
+"Error: Sorted input specified, but the file chromOrderA.bed has the following record with a different sort order than the genomeFile human.hg19.genome
+chr10 10 20 a3 100 +" > exp
+$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted -g human.hg19.genome 2>obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection with -sorted, see that hits are missed
+# With no genome file
+############################################################
+echo " intersect.new.t22...\c"
+echo \
+"chr1 15 20 a1 100 +
+chr2 15 20 a2 100 +
+chrX 15 20 a5 100 +" > exp
+$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection with -sorted, see that hits are correct
+# when sort order of files matches genome file sort order
+############################################################
+echo " intersect.new.t23...\c"
+echo \
+"chr1 15 20 a1 100 +
+chr2 15 20 a2 100 +
+chr10 15 20 a3 100 +
+chr11 15 20 a4 100 +
+chrX 15 20 a5 100 +
+chrM 15 20 a6 100 +" > exp
+$BT intersect -a chromOrderA.bed -b chromOrderB.bed -sorted -g human.hg19.vSort.genome > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bed from file vs b as bed from file
+############################################################
+echo " intersect.new.t24...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_withLargeHeader.bed -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bed from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t25...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_withLargeHeader.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bed from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t26...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_withLargeHeader.bed | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bed from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t27...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_withLargeHeader.bed) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t28...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_withLargeHeader_gzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t29...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_withLargeHeader_gzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t30...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_withLargeHeader_gzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t31...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_withLargeHeader_gzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from file vs b as bed from file
+############################################################
+echo " intersect.new.t32...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a a_withLargeHeader_bgzipped.bed.gz -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from redirect vs b as bed from file
+############################################################
+echo " intersect.new.t33...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a - -b b.bed < a_withLargeHeader_bgzipped.bed.gz > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from pipe vs b as bed from file
+############################################################
+echo " intersect.new.t34...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+cat a_withLargeHeader_bgzipped.bed.gz | $BT intersect -a - -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from fifo vs b as bed from file
+############################################################
+echo " intersect.new.t35...\c"
+echo \
+"chr1 100 101 a2 2 -
+chr1 100 110 a2 2 -" > exp
+$BT intersect -a <(cat a_withLargeHeader_bgzipped.bed.gz) -b b.bed > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test intersection of a with large header as bed from file
+# vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t36...\c"
+$BT intersect -a a_withLargeHeader.bed -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bed from
+# redirect vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t37...\c"
+$BT intersect -a - -b b.bed < a_withLargeHeader.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bed from pipe
+# vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t38...\c"
+cat a_withLargeHeader.bed | $BT intersect -a - -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bed from fifo
+# vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t39...\c"
+$BT intersect -a <(cat a_withLargeHeader.bed) -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from
+# file vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t40...\c"
+$BT intersect -a a_withLargeHeader_gzipped.bed.gz -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from
+# redirect vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t41...\c"
+$BT intersect -a - -b b.bed < a_withLargeHeader_gzipped.bed.gz -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from
+# pipe vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t42...\c"
+cat a_withLargeHeader_gzipped.bed.gz | $BT intersect -a - -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as gzipped from
+# fifo vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t43...\c"
+$BT intersect -a <(cat a_withLargeHeader_gzipped.bed.gz) -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from
+# file vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t44...\c"
+$BT intersect -a a_withLargeHeader_bgzipped.bed.gz -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from
+# redirect vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t45...\c"
+$BT intersect -a - -b b.bed < a_withLargeHeader_bgzipped.bed.gz -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from
+# pipe vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t46...\c"
+cat a_withLargeHeader_bgzipped.bed.gz | $BT intersect -a - -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test intersection of a with large header as bgzipped from
+# fifo vs b as bed from file, and print header
+############################################################
+echo " intersect.new.t47...\c"
+$BT intersect -a <(cat a_withLargeHeader_bgzipped.bed.gz) -b b.bed -header > obs
+check obs aWithHeaderVsB.txt
+rm obs
+
+
+###########################################################
+# Test enforcement of sort order when using -sorted option.
+# Show that detect chrom "jumping", i.e. chr1, chr2, then
+# back to chr1
+############################################################
+echo " intersect.new.t48...\c"
+echo "Error: Sorted input specified" > exp
+$BT intersect -a chromsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 -d ',' > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test enforcement of sort order when using -sorted option.
+# Show that detect chrom "jumping", i.e. chr1, chr2, then
+# back to chr1
+############################################################
+echo " intersect.new.t49...\c"
+echo "Error: Sorted input specified" > exp
+$BT intersect -a recordsOutOfOrder.bed -b b.bed -sorted 2>&1 > /dev/null | grep "Error: Sorted input specified, " | cut -f1 -d ',' > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test that we throw an error for non-existant files
+############################################################
+echo " intersect.new.t50...\c"
+echo "Error: Unable to open file nonExistantFile.bed. Exiting." > exp
+$BT intersect -a nonExistantFile.bed -b b.bed -sorted 2>&1 > /dev/null | cat - >obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test that we allow empty query files
+############################################################
+echo " intersect.new.t51...\c"
+touch exp
+touch dummy.txt
+$BT intersect -a dummy.txt -b b.bed 2>&1 > /dev/null | cat - > obs
+check obs exp
+rm obs exp dummy.txt
+
+
+###########################################################
+# Test that we throw an error for unrecognized arguments
+############################################################
+echo " intersect.new.t52...\c"
+echo "***** ERROR: Unrecognized parameter: -wrongArg *****" > exp
+$BT intersect -a a.bed -b b.bed -wrongArg 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that we can process a Bam file with no text in
+# it's header.
+############################################################
+echo " intersect.new.t53...\c"
+$BT intersect -a gdc.bam -b gdc.bam -bed > obs
+check obs gdc_exp
+rm obs
+
+###########################################################
+# Test that if the query is BAM, and bed output is not
+# explicit, and they asked for an output option that is not
+# valid with BAM output, an error is thrown.
+############################################################
+echo " intersect.new.t54...\c"
+echo "***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****" > exp
+$BT intersect -a a.bam -b b.bed -wao 2>&1 > /dev/null | head -2 | tail -1 > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# Test that gff files work correctly
+############################################################
+echo " intersect.new.t55...\c"
+echo \
+"chr2L . UTR 50 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
+chr2L . CDS 71 100 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
+chr2L . exon 50 100 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
+chr2L . mRNA 50 100 0 + . ID=mRNA:xs2;Parent=g2;
+chr2L . gene 50 100 0 + . ID=g2;" > exp
+$BT intersect -a gdc.gff -b gdc_one.bed > obs
+check obs exp
+rm obs exp
+
+###########################################################
+# Test that we allow empty database files, unsorted
+############################################################
+echo " intersect.new.t56...\c"
+touch exp
+touch dummy.txt
+$BT intersect -a a.bed -b dummy.txt 2>&1 > /dev/null | cat - > obs
+check obs exp
+rm obs exp dummy.txt
+
+###########################################################
+# Test that we allow empty database files, sorted
+############################################################
+echo " intersect.new.t57...\c"
+touch exp
+touch dummy.txt
+$BT intersect -a a.bed -b dummy.txt -sorted 2>&1 > /dev/null | cat - > obs
+check obs exp
+rm obs exp dummy.txt
+
+
+###########################################################
+# Test that we allow empty database files, unsorted, with
+# -v (noHit) option
+############################################################
+echo " intersect.new.t58...\c"
+touch dummy.txt
+$BT intersect -a a.bed -b dummy.txt -v > obs
+check obs a.bed
+rm obs dummy.txt
+
+
+###########################################################
+# Test that an empty query with header run with -header
+# option will print header
+############################################################
+echo " intersect.new.t59...\c"
+echo "#Random Header" >dummy.txt
+$BT intersect -a dummy.txt -b a.bed -header > obs
+check obs dummy.txt
+rm obs dummy.txt
+
+
+###########################################################
+# Test that an empty query with header, gzipped, that
+# runs with -header option will print header
+############################################################
+echo " intersect.new.t60...\c"
+echo "#Random Header" >dummy.txt
+gzip dummy.txt
+echo "#Random Header" >exp
+$BT intersect -a dummy.txt.gz -b a.bed -header > obs
+check obs exp
+rm obs dummy.txt.gz exp
+
+###########################################################
+# Test that an empty query with header, bgzipped, that
+# runs with -header option will print header
+############################################################
+echo " intersect.new.t61...\c"
+echo "#Random Header" >dummy.txt
+bgzip dummy.txt
+echo "#Random Header" >exp
+$BT intersect -a dummy.txt.gz -b a.bed -header > obs
+check obs exp
+rm obs dummy.txt.gz exp
+
+
+###########################################################
+# Test that an empty VCF query with header that
+# runs with -header option will print header
+############################################################
+echo " intersect.new.t62...\c"
+$BT intersect -a headerOnly.vcf -b a.bed -header > obs
+check obs headerOnly.vcf
+rm obs
+
+
+###########################################################
+# Test that files with DOS newline characters, '\r',
+# and/or extra tabs at end of line are handled
+############################################################
+echo " intersect.new.t63...\c"
+echo \
+"chr1 11323785 11617177
+chr1 12645605 13926923
+chr1 14750216 15119039" >exp
+~/mergeBugSpace/bt2-merge-debug/bin/bedtools intersect -a dosLineChar_a.bed -b dosLineCharWithExtraTab_b.bed -v > obs
+check exp obs
+rm exp obs
+
+###########################################################
+# Test that files with no newlines at all are handled
+############################################################
+echo " intersect.new.t64...\c"
+echo "chr17 7577068 7577157" > exp
+$BT intersect -a oneRecordNoNewline.bed -b oneRecordNoNewline.bed > obs
+check obs exp
+rm obs exp
+
diff --git a/test/intersect/performanceTest.sh b/test/intersect/performanceTest.sh
index 6e9109343ee1044af7bdc66a90ae2353ae0c1390..0d63763f6a18fd64611408df356324ec5d02cc21 100755
--- a/test/intersect/performanceTest.sh
+++ b/test/intersect/performanceTest.sh
@@ -23,7 +23,7 @@ if true; then
echo "generating data..."
mkdir perfData
cd perfData
- ../$BT random -l 1000 -n 20000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed
+ ../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > a10M.bed
../$BT random -l 1000 -n 10000000 -g ../human.hg19.genome | sort -k1,1 -k2,2n > b10M.bed
cp a10M.bed a10M_gzipped.bed
gzip a10M_gzipped.bed
diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh
index e6c2c670e1e78fd2ab66d6f6f25bbbca8129f6a0..f29ac8406fafb56731c40c84dfff7a02ae1d3cd6 100644
--- a/test/intersect/test-intersect.sh
+++ b/test/intersect/test-intersect.sh
@@ -458,4 +458,9 @@ chr1 100 200 a2 2 -" > exp
$BT intersect -a a.bed -b a.bam > obs
-rm one_block.bam two_blocks.bam three_blocks.bam
\ No newline at end of file
+rm one_block.bam two_blocks.bam three_blocks.bam
+
+
+cd multi_intersect
+bash test-multi_intersect.sh
+cd ..
\ No newline at end of file