diff --git a/Makefile b/Makefile
index f3cfb4fc399744c40d09b06bc50f8646b5f3d024..139988be1dae1d5c62c3a8148e28fbdb8ed18a4b 100644
--- a/Makefile
+++ b/Makefile
@@ -86,7 +86,8 @@ UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile \
$(SRC_DIR)/utils/BlockedIntervals \
$(SRC_DIR)/utils/Fasta \
$(SRC_DIR)/utils/VectorOps \
- $(SRC_DIR)/utils/GenomeFile
+ $(SRC_DIR)/utils/GenomeFile \
+ $(SRC_DIR)/utils/RecordOutputMgr
BUILT_OBJECTS = $(OBJ_DIR)/*.o
diff --git a/src/intersectFile/Makefile b/src/intersectFile/Makefile
index e8ac9ea59f32f81ed62311c5d49259c33feac41c..e265b3348d1b1883c8f46e15b2902e3f2e5f8933 100644
--- a/src/intersectFile/Makefile
+++ b/src/intersectFile/Makefile
@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/NewChromsweep \
-I$(UTILITIES_DIR)/BinTree \
-I$(UTILITIES_DIR)/version/
diff --git a/src/intersectFile/intersectFile.cpp b/src/intersectFile/intersectFile.cpp
index 5c78887425de2e8a7712aac3ba69e41db86a56ac..928d1d9a4f7e8f985cc9edd2ca44b1dbdcf8a517 100644
--- a/src/intersectFile/intersectFile.cpp
+++ b/src/intersectFile/intersectFile.cpp
@@ -24,18 +24,16 @@ FileIntersect::FileIntersect(ContextIntersect *context)
_recordOutputMgr(NULL)
{
_recordOutputMgr = new RecordOutputMgr();
+ _recordOutputMgr->init(_context);
if (_context->getObeySplits()) {
- _blockMgr = new BlockMgr();
- _blockMgr->setContext(context);
+ _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
_recordOutputMgr->setSplitInfo(_blockMgr);
}
}
FileIntersect::~FileIntersect(void) {
- if (_blockMgr != NULL) {
- delete _blockMgr;
- _blockMgr = NULL;
- }
+ delete _blockMgr;
+ _blockMgr = NULL;
delete _recordOutputMgr;
}
@@ -59,9 +57,6 @@ bool FileIntersect::processSortedFiles()
if (!sweep.init()) {
return false;
}
- if (!_recordOutputMgr->init(_context)) {
- return false;
- }
RecordKeyList hitSet;
while (sweep.next(hitSet)) {
@@ -79,23 +74,11 @@ bool FileIntersect::processSortedFiles()
bool FileIntersect::processUnsortedFiles()
{
- const QuickString &databaseFilename = _context->getDatabaseFileName();
- BinTree *binTree = new BinTree(_context->getDatabaseFileIdx(), _context);
-
- FileRecordMgr *queryFRM = new FileRecordMgr(_context->getQueryFileIdx(), _context);
- if (!queryFRM->open()) {
- return false;
- }
-
- if (!binTree->loadDB()) {
- fprintf(stderr, "Error: Unable to load database file %s.\n", databaseFilename.c_str());
- delete binTree;
- exit(1);
- }
+ BinTree *binTree = new BinTree( _context);
+ binTree->loadDB();
+ FileRecordMgr *queryFRM = _context->getFile(_context->getQueryFileIdx());
- _context->determineOutputType();
- _recordOutputMgr->init(_context);
while (!queryFRM->eof()) {
Record *queryRecord = queryFRM->allocateAndGetNextRecord();
@@ -117,7 +100,6 @@ bool FileIntersect::processUnsortedFiles()
queryFRM->close();
//clean up.
- delete queryFRM;
delete binTree;
return true;
}
diff --git a/src/mapFile/Makefile b/src/mapFile/Makefile
index 3eea8d065b54983bd7a1fea9d2f8ecad708fe54a..17bb42df2d5c71d7eae0093ef8013c57c3fce42d 100644
--- a/src/mapFile/Makefile
+++ b/src/mapFile/Makefile
@@ -28,6 +28,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/NewChromsweep \
-I$(UTILITIES_DIR)/VectorOps \
-I$(UTILITIES_DIR)/BinTree \
diff --git a/src/mapFile/mapFile.cpp b/src/mapFile/mapFile.cpp
index 3bd133d2b4fb13c01d58eecaa97dd9e48e091a37..88dcc26fe8eb24eacf8108a577e8ab4e757b201b 100644
--- a/src/mapFile/mapFile.cpp
+++ b/src/mapFile/mapFile.cpp
@@ -23,18 +23,16 @@ FileMap::FileMap(ContextMap *context)
_blockMgr(NULL),
_recordOutputMgr(NULL)
{
- // FIX ME - block manager only works for intersect
- //_blockMgr = new BlockMgr();
- //_blockMgr->setContext(context);
+ _blockMgr = new BlockMgr(_context->getOverlapFraction(), _context->getReciprocal());
_recordOutputMgr = new RecordOutputMgr();
+ _recordOutputMgr->init(_context);
}
FileMap::~FileMap(void) {
- if (_blockMgr != NULL) {
- delete _blockMgr;
- _blockMgr = NULL;
- }
- delete _recordOutputMgr;
+ delete _blockMgr;
+ _blockMgr = NULL;
+ delete _recordOutputMgr;
+ _recordOutputMgr = NULL;
}
bool FileMap::mapFiles()
@@ -43,20 +41,18 @@ bool FileMap::mapFiles()
if (!sweep.init()) {
return false;
}
- if (!_recordOutputMgr->init(_context)) {
- return false;
- }
RecordKeyList hitSet;
while (sweep.next(hitSet)) {
- //if (_context->getObeySplits()) {
- // RecordKeyList keySet(hitSet.getKey());
- // RecordKeyList resultSet(hitSet.getKey());
- // _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
- //} else {
- //}
- //_recordOutputMgr->printKeyAndTerminate(hitSet);
- SummarizeHits(hitSet);
- _recordOutputMgr->printRecord(hitSet.getKey(), _output);
+ if (_context->getObeySplits()) {
+ RecordKeyList keySet(hitSet.getKey());
+ RecordKeyList resultSet(hitSet.getKey());
+ _blockMgr->findBlockedOverlaps(keySet, hitSet, resultSet);
+ SummarizeHits(resultSet);
+ _recordOutputMgr->printRecord(resultSet.getKey(), _output);
+ } else {
+ SummarizeHits(hitSet);
+ _recordOutputMgr->printRecord(hitSet.getKey(), _output);
+ }
}
return true;
}
@@ -116,7 +112,7 @@ void FileMap::SummarizeHits(RecordKeyList &hits) {
else if (operation == "distinct")
_tmp_output << vo.GetDistinct();
else {
- cerr << "ERROR: " << operation << " is an unrecoginzed operation\n";
+ cerr << "ERROR: " << operation << " is an unrecognized operation\n";
exit(1);
}
_output.append(_tmp_output.str());
diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp
index fe87c9f3d96cc6b1b98b69607f6a40affab05597..a9eeb36990267c69e78b473f8824483b75629cb6 100644
--- a/src/mapFile/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -215,6 +215,8 @@ void map_help(void) {
cerr << "\t\tthat overlap A on the _opposite_ strand." << endl;
cerr << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+ cerr << "\t-split\t" << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
cerr << "\t-g\t" << "Provide a genome file to enforce consistent chromosome sort order" << endl;
cerr <<"\t\tacross input files." << endl << endl;
diff --git a/src/nekSandbox1/nekSandboxMain.cpp b/src/nekSandbox1/nekSandboxMain.cpp
index 3a5449ff6077bc8404180213415d11dfb87b2f2f..ac3fb3196b49d602e98a2e79ae369ef907573603 100644
--- a/src/nekSandbox1/nekSandboxMain.cpp
+++ b/src/nekSandbox1/nekSandboxMain.cpp
@@ -128,36 +128,36 @@ int nek_sandbox1_main(int argc,char** argv)
//
// return 0;
//
- ContextIntersect context;
- context.addInputFile(argv[1]);
- context.setSortedInput(true);
-// context.setObeySplits(true);
-
- FileRecordMgr frm(0, &context);
-// frm.getBlockMgr()->setBreakOnSkipOps(true);
- if (!frm.open()) {
- cerr << "Error: couldn't open file " << argv[1] << ". Exiting." << endl;
- exit(1);
- }
- cout << "File Type is : " << frm.getFileType() << ", " << frm.getFileTypeName() << "." << endl;
- cout << "RecordType is : " << frm.getRecordType() << ", " << frm.getRecordTypeName() << "." << endl;
-
- bool headerFound = false;
- QuickString outbuf;
- while (!frm.eof()) {
- Record *record = frm.allocateAndGetNextRecord();
- if (!headerFound && frm.hasHeader()) {
- cout << frm.getHeader() << endl;
- headerFound = true;
- }
- if (record == NULL) {
- break;
- }
-
- outbuf.clear();
- record->print(outbuf);
- printf("%s\n", outbuf.c_str());
-
+// ContextIntersect context;
+// context.addInputFile(argv[1]);
+// context.setSortedInput(true);
+//// context.setObeySplits(true);
+//
+// FileRecordMgr frm(0, &context);
+//// frm.getBlockMgr()->setBreakOnSkipOps(true);
+// if (!frm.open()) {
+// cerr << "Error: couldn't open file " << argv[1] << ". Exiting." << endl;
+// exit(1);
+// }
+// cout << "File Type is : " << frm.getFileType() << ", " << frm.getFileTypeName() << "." << endl;
+// cout << "RecordType is : " << frm.getRecordType() << ", " << frm.getRecordTypeName() << "." << endl;
+//
+// bool headerFound = false;
+// QuickString outbuf;
+// while (!frm.eof()) {
+// Record *record = frm.allocateAndGetNextRecord();
+// if (!headerFound && frm.hasHeader()) {
+// cout << frm.getHeader() << endl;
+// headerFound = true;
+// }
+// if (record == NULL) {
+// break;
+// }
+//
+// outbuf.clear();
+// record->print(outbuf);
+// printf("%s\n", outbuf.c_str());
+//
// RecordKeyList recList(record);
// int blockCount = frm.getBlockMgr()->getBlocks(recList);
// printf("The %d blocks are:\n", blockCount);
@@ -168,10 +168,10 @@ int nek_sandbox1_main(int argc,char** argv)
// printf("\n\n");
// frm.getBlockMgr()->deleteBlocks(recList);
- frm.deleteRecord(record);
- }
+// frm.deleteRecord(record);
+// }
// cout << "Final header is: " << frm.getHeader() << endl;
- frm.close();
+// frm.close();
return 0;
}
diff --git a/src/sampleFile/Makefile b/src/sampleFile/Makefile
index 5c20a9c56e2450c6c67fa35efb79041e576c6525..2042291e68735b4316062d64a04e7f35d9847b2a 100644
--- a/src/sampleFile/Makefile
+++ b/src/sampleFile/Makefile
@@ -17,6 +17,7 @@ INCLUDES = -I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
diff --git a/src/sampleFile/SampleFile.cpp b/src/sampleFile/SampleFile.cpp
index 8f532c5f47a8eb89da81fac4d5c3a35f15a17187..8291824cef1cb5a67d7827c9bf0e867b7df4f48f 100644
--- a/src/sampleFile/SampleFile.cpp
+++ b/src/sampleFile/SampleFile.cpp
@@ -35,11 +35,7 @@ SampleFile::~SampleFile() {
bool SampleFile::takeSample()
{
//we're only operating on one file, so the idx is zero.
- _inputFile = new FileRecordMgr(0, _context);
- if (!_inputFile->open()) {
- return false; // FRM will give the error and die anyway,
- //no error message needed here.
- }
+ _inputFile = _context->getFile(0);
_samples.resize(_numSamples, NULL);
@@ -50,7 +46,6 @@ bool SampleFile::takeSample()
_context->getUnspecifiedSeed();
}
- _context->determineOutputType();
_outputMgr = new RecordOutputMgr();
_outputMgr->init(_context);
@@ -82,10 +77,6 @@ bool SampleFile::takeSample()
}
delete _outputMgr;
_inputFile->close();
-
- //clean up.
- delete _inputFile;
-
return true;
}
diff --git a/src/utils/BinTree/BinTree.cpp b/src/utils/BinTree/BinTree.cpp
index e7a1fde481700340b646f7457ec1bc8d77712c57..54696f6928e7667683d993c658f7771d8e88ff2f 100644
--- a/src/utils/BinTree/BinTree.cpp
+++ b/src/utils/BinTree/BinTree.cpp
@@ -2,11 +2,10 @@
#include "FileRecordMgr.h"
-BinTree::BinTree(int databaseFileIdx, ContextIntersect *context)
-: _databaseFileIdx(databaseFileIdx),
+BinTree::BinTree(ContextIntersect *context)
+: _databaseFile(NULL),
_context(context),
_binOffsetsExtended(NULL),
- _dbFileMgr(NULL),
_showBinMetrics(false),
_maxBinNumFound(0)
{
@@ -37,7 +36,7 @@ BinTree::~BinTree() {
}
for (innerListIterType listIter = bin->begin(); listIter != bin->end(); listIter = bin->next()) {
const Record *record = listIter->value();
- _dbFileMgr->deleteRecord(record);
+ _databaseFile->deleteRecord(record);
}
delete bin;
bin = NULL;
@@ -46,10 +45,6 @@ BinTree::~BinTree() {
delete [] bins;
bins = NULL;
}
- if (_dbFileMgr != NULL) {
- delete _dbFileMgr;
- _dbFileMgr = NULL;
- }
delete [] _binOffsetsExtended;
if (_showBinMetrics) {
@@ -73,18 +68,13 @@ BinTree::~BinTree() {
}
}
-bool BinTree::loadDB()
+void BinTree::loadDB()
{
- _dbFileMgr = new FileRecordMgr(_databaseFileIdx, _context);
- if (!_dbFileMgr->open()) {
- fprintf(stderr, "ERROR: Can't open database file %s to build tree.\n", _context->getInputFileName(_databaseFileIdx).c_str());
- delete _dbFileMgr;
- _dbFileMgr = NULL;
- return false;
- }
+ _databaseFile = _context->getFile(_context->getDatabaseFileIdx());
+
Record *record = NULL;
- while (!_dbFileMgr->eof()) {
- record = _dbFileMgr->allocateAndGetNextRecord();
+ while (!_databaseFile->eof()) {
+ record = _databaseFile->allocateAndGetNextRecord();
//In addition to NULL records, we also don't want to add unmapped reads.
if (record == NULL || record->isUnmapped()) {
continue;
@@ -92,19 +82,17 @@ bool BinTree::loadDB()
if (!addRecordToTree(record)) {
fprintf(stderr, "ERROR: Unable to add record to tree.\n");
- _dbFileMgr->close();
- return false;
+ _databaseFile->close();
+ exit(1);
}
}
- _dbFileMgr->close();
+ _databaseFile->close();
//TBD: give ERROR and return false if tree is empty.
if (_mainMap.empty()) {
fprintf(stderr, "ERROR: Tree is empty, no records added.\n");
- return false;
+ exit(1);
}
- return true;
-
}
void BinTree::getHits(Record *record, RecordKeyList &hitSet)
diff --git a/src/utils/BinTree/BinTree.h b/src/utils/BinTree/BinTree.h
index 800fc0e3ca1c23168cc1337852b9e1a557a37f09..ce15c481e9831cc4bd95f544bb4f3585084e956b 100644
--- a/src/utils/BinTree/BinTree.h
+++ b/src/utils/BinTree/BinTree.h
@@ -24,15 +24,15 @@ class Record;
class BinTree {
public:
- BinTree(int databaseFileIdx, ContextIntersect *context);
+ BinTree(ContextIntersect *context);
~BinTree();
- bool loadDB();
+ void loadDB();
void getHits(Record *record, RecordKeyList &hitSet);
private:
- int _databaseFileIdx;
+ FileRecordMgr *_databaseFile;
ContextIntersect *_context;
//
@@ -60,8 +60,6 @@ private:
typedef map<mainKeyType, allBinsType> mainMapType;
mainMapType _mainMap;
- FileRecordMgr *_dbFileMgr;
-
bool _showBinMetrics;
uint32_t _maxBinNumFound;
map<uint32_t, int> _binsHit;
diff --git a/src/utils/Contexts/Context.cpp b/src/utils/Contexts/Context.cpp
deleted file mode 100644
index 439c1fef8931460ea24540b42cc10fe3d38757ce..0000000000000000000000000000000000000000
--- a/src/utils/Contexts/Context.cpp
+++ /dev/null
@@ -1,451 +0,0 @@
-/*
- * Context.cpp
- *
- * Created on: Feb 12, 2013
- * Author: nek3d
- */
-
-#include "Context.h"
-#include <unistd.h>
-#include <sys/types.h>
-
-Context::Context()
-:
- _program(UNSPECIFIED_PROGRAM),
- _useMergedIntervals(false),
- _genomeFile(NULL),
- _outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
- _outputTypeDetermined(false),
- _skipFirstArgs(0),
- _showHelp(false),
- _obeySplits(false),
- _uncompressedBam(false),
- _useBufferedOutput(true),
- _anyHit(false),
- _noHit(false),
- _writeA(false),
- _writeB(false),
- _leftJoin(false),
- _writeCount(false),
- _writeOverlap(false),
- _writeAllOverlap(false),
- _haveFraction(false),
- _overlapFraction(1E-9),
- _reciprocal(false),
- _sameStrand(false),
- _diffStrand(false),
- _sortedInput(false),
- _printHeader(false),
- _printable(true),
- _explicitBedOutput(false),
- _queryFileIdx(-1),
- _databaseFileIdx(-1),
- _bamHeaderAndRefIdx(-1),
- _maxNumDatabaseFields(0),
- _useFullBamTags(false),
- _reportCount(false),
- _maxDistance(0),
- _reportNames(false),
- _reportScores(false),
- _numOutputRecords(0),
- _hasConstantSeed(false),
- _seed(0),
- _forwardOnly(false),
- _reverseOnly(false)
-{
- _programNames["intersect"] = INTERSECT;
- _programNames["sample"] = SAMPLE;
-
- _validScoreOps.insert("sum");
- _validScoreOps.insert("max");
- _validScoreOps.insert("min");
- _validScoreOps.insert("mean");
- _validScoreOps.insert("mode");
- _validScoreOps.insert("median");
- _validScoreOps.insert("antimode");
- _validScoreOps.insert("collapse");
-}
-
-Context::~Context()
-{
- if (_genomeFile != NULL) {
- delete _genomeFile;
- _genomeFile = NULL;
- }
-}
-
-bool Context::determineOutputType() {
- if (_outputTypeDetermined) {
- return true;
- }
- //test whether output should be BED or BAM.
- //If the user explicitly requested BED, then it's BED.
- if (getExplicitBedOutput()) {
- setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
- _outputTypeDetermined = true;
- return true;
- }
- //If this is an intersection, and the query is BAM, then
- //the output is BAM.
- if (_program == INTERSECT && getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
- setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
- _outputTypeDetermined = true;
- return true;
-
- }
- //Otherwise, if there are any BAM files in the input,
- //then the output should be BAM.
- for (size_t i = 0; i < _inputFiles.size(); i++) {
- if (_inputFiles[i]._fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
- setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
- _bamHeaderAndRefIdx = i;
- _outputTypeDetermined = true;
- return true;
- }
- }
-
- //Okay, it's bed.
- setOutputFileType(FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE);
- _outputTypeDetermined = true;
- return true;
-
-
-}
-
-void Context::openGenomeFile(const QuickString &genomeFilename)
-{
- _genomeFile = new NewGenomeFile(genomeFilename.c_str());
-}
-
-void Context::openGenomeFile(const BamTools::RefVector &refVector)
-{
- _genomeFile = new NewGenomeFile(refVector);
-}
-
-bool Context::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
- _argc = argc;
- _argv = argv;
- _skipFirstArgs = skipFirstArgs;
- if (argc < 2) {
- setShowHelp(true);
- return false;
- }
-
- setProgram(_programNames[argv[0]]);
-
- _argsProcessed.resize(argc - skipFirstArgs, false);
-
- for (int i=skipFirstArgs; i < argc; i++) {
- if (isUsed(i - skipFirstArgs)) {
- continue;
- }
-
- if (strcmp(argv[i], "-i") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -i option given, but no input file specified. *****";
- return false;
- }
- addInputFile(argv[i+1]);
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- } else if (strcmp(argv[i], "-g") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -g option given, but no genome file specified. *****";
- return false;
- }
- openGenomeFile(argv[i+1]);
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- } else if (strcmp(argv[i], "-h") == 0) {
- setShowHelp(true);
- markUsed(i - skipFirstArgs);
- } else if (strcmp(argv[i], "--help") == 0) {
- setShowHelp(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-split") == 0) {
- setObeySplits(true);
- markUsed(i - skipFirstArgs);
- }
- if (strcmp(argv[i], "-a") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -a option given, but no query file specified. *****";
- return false;
- }
-
- addInputFile(argv[i+1]);
- _queryFileIdx = getNumInputFiles() -1;
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-abam") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -abam option given, but no query BAM file specified. *****";
- return false;
- }
- addInputFile(argv[i+1]);
- _queryFileIdx = getNumInputFiles() -1;
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- setInputFileType(_queryFileIdx, FileRecordTypeChecker::BAM_FILE_TYPE);
- }
- else if (strcmp(argv[i], "-b") == 0) {
- if (argc <= i+1) {
- _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);
- } else if (strcmp(argv[i], "-u") == 0) {
- setAnyHit(true);
- markUsed(i - skipFirstArgs);
- } else if(strcmp(argv[i], "-f") == 0) {
- if ((i+1) < argc) {
- setHaveFraction(true);
- setOverlapFraction(atof(argv[i + 1]));
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- }
- }
- else if(strcmp(argv[i], "-bed") == 0) {
- setExplicitBedOutput(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-wa") == 0) {
- setWriteA(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-wb") == 0) {
- setWriteB(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-wo") == 0) {
- setWriteOverlap(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-wao") == 0) {
- setWriteAllOverlap(true);
- setWriteOverlap(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-c") == 0) {
- setWriteCount(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-r") == 0) {
- setReciprocal(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-v") == 0) {
- setNoHit(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-s") == 0) {
- setSameStrand(true);
- markUsed(i - skipFirstArgs);
-
- if (_program == SAMPLE) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
- return false;
- }
- if (strcmp(argv[i+1], "forward") == 0) {
- _forwardOnly = true;
- } else if (strcmp(argv[i+1], "reverse") == 0) {
- _reverseOnly = true;
- } else {
- _errorMsg = "\n***** ERROR: -s option given, but \"forward\" or \"reverse\" not specified. *****";
- return false;
- }
- i++;
- markUsed(i - skipFirstArgs);
- }
- }
- else if (strcmp(argv[i], "-S") == 0) {
- setDiffStrand(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-loj") == 0) {
- setLeftJoin(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-ubam") == 0) {
- setUncompressedBam(true);
- markUsed(i - skipFirstArgs);
- }
- else if (strcmp(argv[i], "-fbam") == 0) {
- setUseFullBamTags(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-sorted") == 0) {
- setSortedInput(true);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-nobuf") == 0) {
- setUseBufferedOutput(false);
- markUsed(i - skipFirstArgs);
- }
- else if(strcmp(argv[i], "-header") == 0) {
- setPrintHeader(true);
- markUsed(i - skipFirstArgs);
- } else if (strcmp(argv[i], "-n") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -n option given, but no number of output records specified. *****";
- return false;
- }
- setNumOutputRecords(atoi(argv[i + 1]));
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- } else if (strcmp(argv[i], "-seed") == 0) {
- if (argc <= i+1) {
- _errorMsg = "\n***** ERROR: -seed option given, but no seed specified. *****";
- return false;
- }
- _hasConstantSeed = true;
- _seed = atoi(argv[i+1]);
- srand(_seed);
- markUsed(i - skipFirstArgs);
- i++;
- markUsed(i - skipFirstArgs);
- }
- }
- return true;
-}
-
-bool Context::isValidState()
-{
- if (!cmdArgsValid()) {
- return false;
- }
-
- if (_program == INTERSECT) {
- return isValidIntersectState();
- }
- if (_program == SAMPLE) {
- return isValidSampleState();
- }
- return false;
-}
-
-
-bool Context::cmdArgsValid()
-{
- bool retval = true;
- for (int i = _skipFirstArgs; i < _argc; i++) {
- if (!isUsed(i - _skipFirstArgs)) {
- _errorMsg += "\n***** ERROR: Unrecognized parameter: ";
- _errorMsg += _argv[i];
- _errorMsg += " *****";
- retval = false;
- }
- }
- return retval;
-}
-
-int Context::getBamHeaderAndRefIdx() {
- if (_bamHeaderAndRefIdx != -1) {
- //already found which BAM file to use for the header
- return _bamHeaderAndRefIdx;
- }
- if (_inputFiles[_queryFileIdx]._fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
- _bamHeaderAndRefIdx = _queryFileIdx;
- } else {
- _bamHeaderAndRefIdx = _databaseFileIdx;
- }
- return _bamHeaderAndRefIdx;
-}
-
-int Context::getUnspecifiedSeed()
-{
- // thanks to Rob Long for the tip.
- _seed = (unsigned)time(0)+(unsigned)getpid();
- srand(_seed);
- return _seed;
-}
-
-
-bool Context::isValidIntersectState()
-{
- if (_queryFileIdx == -1 || _databaseFileIdx == -1) {
- _errorMsg = "\n***** ERROR: query and database files not specified. *****";
- return false;
- }
-
- if (getAnyHit() && getNoHit()) {
- _errorMsg = "\n***** ERROR: request either -u for anyHit OR -v for noHit, not both. *****";
- return false;
- }
- if (getWriteCount()) {
- if (getAnyHit()) {
- _errorMsg = "\n***** ERROR: request either -c for writeCount OR -u for anyHit, not both. *****";
- return false;
- } else if (getWriteB()) {
- _errorMsg = "\n***** ERROR: request either -c for writeCount OR -wb for writeB, not both. *****";
- return false;
- } else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
- _errorMsg = "\n***** ERROR: writeCount option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
- return false;
- }
- }
- if (getWriteOverlap()) {
-
- if (getWriteA()) {
- _errorMsg = "\n***** ERROR: request either -wa for writeA OR -wo for writeOverlap, not both. *****";
- return false;
- } else if (getWriteB()) {
- _errorMsg = "\n***** ERROR: request either -wb for writeB OR -wo for writeOverlap, not both. *****";
- return false;
- } else if (getWriteCount()) {
- _errorMsg = "\n***** ERROR: request either -c for writeCount OR -wo for writeOverlap, not both. *****";
- return false;
- } else if (getAnyHit()) {
- _errorMsg = "\n***** ERROR: request either -u for anyHit OR -wo for writeOverlap, not both. *****";
- return false;
- } else if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
- _errorMsg = "\n***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****";
- return false;
- }
- }
- if (getWriteB() || getLeftJoin()) {
- if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
- cerr << endl << "*****" << endl << "*****WARNING: -wb and -loj are ignored with bam input, unless bed output is specified with -bed option." << endl << "*****" << endl;
- }
- }
- if (getSameStrand() && getDiffStrand()) {
- _errorMsg = "\n***** ERROR: request -s for sameStrand, or -S for diffStrand, not both. *****";
- return false;
- }
-
- if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && getPrintHeader()) {
- cerr << endl << "*****" << endl << "*****WARNING: -header option is not valid for BAM input." << endl << "*****" << endl;
- setPrintHeader(false);
- }
- if (getAnyHit() || getNoHit() || getWriteCount()) {
- setPrintable(false);
- }
- return _inputFiles.size() > 0;
-}
-
-bool Context::isValidSampleState()
-{
- if (_inputFiles.size() != 1) {
- _errorMsg = "\n***** ERROR: input file not specified. *****";
- // Allow one and only input file for now
- return false;
- }
-// if (_numOutputRecords < 1) {
-// _errorMsg = "\n***** ERROR: number of output records not specified. *****";
-// return false;
-// }
- return true;
-}
-
diff --git a/src/utils/Contexts/Context.h b/src/utils/Contexts/Context.h
deleted file mode 100644
index 19160e9556936d3e6907c147d7653be35b3069d8..0000000000000000000000000000000000000000
--- a/src/utils/Contexts/Context.h
+++ /dev/null
@@ -1,293 +0,0 @@
-/*
- * ContextBase.h
- *
- * Created on: Feb 11, 2013
- * Author: nek3d
- */
-
-#ifndef CONTEXTBASE_H_
-#define CONTEXTBASE_H_
-
-
-// The Context class handles the settings for an operation,
-// such as merge, intersect, jaccard, etc.
-//
-// Settings include the input and output parameters, such as input
-// files, file types (if explicitly provided), genome files,
-// run options, output format, etc.
-
-#include <cstdlib>
-#include "version.h"
-#include "BedtoolsTypes.h"
-#include "FileRecordTypeChecker.h"
-#include "NewGenomeFile.h"
-#include "api/BamReader.h"
-#include "api/BamAux.h"
-
-
-class Context {
-public:
- Context();
- ~Context();
-
- typedef FileRecordTypeChecker::FILE_TYPE ContextFileType;
- typedef FileRecordTypeChecker::RECORD_TYPE ContextRecordType;
-
- typedef enum {UNSPECIFIED_PROGRAM, INTERSECT, WINDOW, CLOSEST, COVERAGE, MAP, GENOMECOV, MERGE, CLUSTER,
- COMPLEMENT, SUBTRACT, SLOP, FLANK, SORT, RANDOM, SAMPLE, SHUFFLE, ANNOTATE, MULTIINTER, UNIONBEDG, PAIRTOBED,
- PAIRTOPAIR,BAMTOBED, BEDTOBAM, BEDTOFASTQ, BEDPETOBAM, BED12TOBED6, GETFASTA, MASKFASTA, NUC,
- MULTICOV, TAG, JACCARD, OVERLAP, IGV, LINKS,MAKEWINDOWS, GROUPBY, EXPAND } PROGRAM_TYPE;
-
- PROGRAM_TYPE getProgram() const { return _program; }
- void setProgram(PROGRAM_TYPE program) { _program = program; }
-
- void addInputFile(const QuickString &inputFile,
- ContextFileType explicitFileType = FileRecordTypeChecker::UNKNOWN_FILE_TYPE,
- ContextRecordType explicitRecordType = FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
- _inputFiles.push_back(FileEntryType(inputFile, explicitFileType, explicitRecordType));
- }
-
- int getNumInputFiles() const { return _inputFiles.size(); }
- const QuickString &getInputFileName(int fileNum) const { return _inputFiles[fileNum]._fileName; }
- ContextFileType getInputFileType(int fileNum) const { return _inputFiles[fileNum]._fileType; }
- void setInputFileType(int fileNum, ContextFileType fileType) { _inputFiles[fileNum]._fileType = fileType; }
- ContextRecordType getInputRecordType(int fileNum) const { return _inputFiles[fileNum]._recordType; }
- void setInputRecordType(int fileNum, ContextRecordType recordType) { _inputFiles[fileNum]._recordType = recordType; }
- //HERE ARE SOME SIMPLER VERSIONS OF THE ABOVE FOR APPS THAT HAVE ONLY ONE INPUT FILE
- const QuickString &getInputFileName() const { return _inputFiles[0]._fileName; }
- ContextFileType getInputFileType() const { return _inputFiles[0]._fileType; }
- void setInputFileType(ContextFileType fileType) { _inputFiles[0]._fileType = fileType; }
- ContextRecordType getInputRecordType() const { return _inputFiles[0]._recordType; }
- void setInputRecordType(ContextRecordType recordType) { _inputFiles[0]._recordType = recordType; }
- int getInputFileIdx() const { return 0; }
-
-
-
-
- bool determineOutputType();
-
- const QuickString &getHeader(int fileIdx) { return _headers[fileIdx]; }
- void setHeader(int fileIdx, const QuickString &header) { _headers[fileIdx] = header; }
- const BamTools::RefVector &getReferences(int fileIdx) { return _references[fileIdx]; }
- void setReferences(int fileIdx, const BamTools::RefVector &refs) { _references[fileIdx] = refs; }
- int getBamHeaderAndRefIdx(); //return idx of 1st query that is BAM. If none, first DB that is BAM.
-
- bool getUseMergedIntervals() const { return _useMergedIntervals; }
- void setUseMergedIntervals(bool val) { _useMergedIntervals = val; }
-
- void openGenomeFile(const QuickString &genomeFilename);
- void openGenomeFile(const BamTools::RefVector &refVector);
- bool hasGenomeFile() const { return _genomeFile != NULL; }
- NewGenomeFile *getGenomeFile() const { return _genomeFile; }
-
- void setOutputFileType(ContextFileType fileType) { _outputFileType = fileType; }
- ContextFileType getOutputFileType() const { return _outputFileType; }
-
- bool parseCmdArgs(int argc, char **argv, int skipFirstArgs);
-
- //isValidState checks that parameters to context are in an acceptable state.
- // If not, the error msg string will be set with a reason why it failed.
- bool isValidState();
- bool getShowHelp() const { return _showHelp; }
- void setShowHelp(bool val) { _showHelp = val; }
-
- const QuickString &getErrorMsg() const { return _errorMsg; }
- void setErrorMessage(const QuickString &errorMsg) { _errorMsg = errorMsg; }
-
- //split handling.
- bool getObeySplits() const {return _obeySplits; }
- void setObeySplits(bool val) { _obeySplits = val; }
-
- //Decide whether output format is BED or BAM.
- //Default is BAM if any input files are BAM.
- bool getExplicitBedOutput() const { return _explicitBedOutput; }
- void setExplicitBedOutput(bool val) { _explicitBedOutput = val; }
-
- bool getUncompressedBam() const { return _uncompressedBam; }
- void setUncompressedBam(bool val) { _uncompressedBam = val; }
-
- bool getUseBufferedOutput() const { return _useBufferedOutput; }
- void setUseBufferedOutput(bool val) { _useBufferedOutput = val; }
- //
- // INTERSECT METOHDS
- //
- //NOTE: Query and database files will only be marked as such by either the
- //parseCmdArgs method, or by explicitly setting them.
- int getQueryFileIdx() const { return _queryFileIdx; }
- void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
- int getDatabaseFileIdx() const { return _databaseFileIdx; }
- void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
- const QuickString &getQueryFileName() const { return _inputFiles[_queryFileIdx]._fileName; }
- const QuickString &getDatabaseFileName() const { return _inputFiles[_databaseFileIdx]._fileName; }
- ContextFileType getQueryFileType() const { return _inputFiles[_queryFileIdx]._fileType; }
- ContextFileType getDatabaseFileType() const { return _inputFiles[_databaseFileIdx]._fileType; }
- ContextRecordType getQueryRecordType() const { return _inputFiles[_queryFileIdx]._recordType; }
- ContextRecordType getDatabaseRecordType() const { return _inputFiles[_databaseFileIdx]._recordType; }
- int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
- void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
-
- bool getAnyHit() const {return _anyHit; }
- void setAnyHit(bool val) { _anyHit = val; }
-
- bool getNoHit() const {return _noHit; }
- void setNoHit(bool val) { _noHit = val; }
-
- bool getLeftJoin() const {return _leftJoin; }
- void setLeftJoin(bool val) { _leftJoin = val; }
-
- bool getWriteA() const {return _writeA; }
- void setWriteA(bool val) { _writeA = val; }
-
- bool getWriteB() const {return _writeB; }
- void setWriteB(bool val) { _writeB = val; }
-
- bool getWriteCount() const {return _writeCount; }
- void setWriteCount(bool val) { _writeCount = val; }
-
- bool getWriteOverlap() const {return _writeOverlap; }
- void setWriteOverlap(bool val) { _writeOverlap = val; }
-
- bool getWriteAllOverlap() const {return _writeAllOverlap; }
- void setWriteAllOverlap(bool val) { _writeAllOverlap = val; }
-
- bool getHaveFraction() const {return _haveFraction; }
- void setHaveFraction(bool val) { _haveFraction = val; }
-
- float getOverlapFraction() const { return _overlapFraction; }
- void setOverlapFraction(float fraction) { _overlapFraction = fraction; }
-
- bool getReciprocal() const {return _reciprocal; }
- void setReciprocal(bool val) { _reciprocal = val; }
-
- bool getSameStrand() const {return _sameStrand; }
- void setSameStrand(bool val) { _sameStrand = val; }
- bool getForwardOnly() const { return _forwardOnly; }
- bool getReverseOnly() const { return _reverseOnly; }
-
- bool getDiffStrand() const {return _diffStrand; }
- void setDiffStrand(bool val) { _diffStrand = val; }
-
- bool getSortedInput() const {return _sortedInput; }
- void setSortedInput(bool val) { _sortedInput = val; }
-
- bool getPrintHeader() const {return _printHeader; }
- void setPrintHeader(bool val) { _printHeader = val; }
-
- bool getPrintable() const { return _printable; }
- void setPrintable(bool val) { _printable = val; }
-
- bool getUseFullBamTags() const { return _useFullBamTags; }
- void setUseFullBamTags(bool val) { _useFullBamTags = val; }
-
- //
- // MERGE METHODS
- //
- bool getReportCount() const { return _reportCount; }
- void setReportCount(bool val) { _reportCount = val; }
-
- int getMaxDistance() const { return _maxDistance; }
- void setMaxDistance(int distance) { _maxDistance = distance; }
-
- bool getReportNames() const { return _reportNames; }
- void setReportNames(bool val) { _reportNames = val; }
-
- bool getReportScores() const { return _reportScores; }
- void setReportScores(bool val) { _reportScores = val; }
-
- const QuickString &getScoreOp() const { return _scoreOp; }
- void setScoreOp(const QuickString &op) { _scoreOp = op; }
-
-
- // METHODS FOR PROGRAMS WITH USER_SPECIFIED NUMBER
- // OF OUTPUT RECORDS.
- int getNumOutputRecords() const { return _numOutputRecords; }
- void setNumOutputRecords(int val) { _numOutputRecords = val; }
-
- //SEED OPS FOR APPS WITH RANDOMNESS
- //When a seed has been specified on the command line, srand
- //will have been already been called during command line parsing.
- //For reference, srand is the C function that initializes the
- //psuedo-random number generator. If a seed has not been
- //specifified, the user may call the
- bool hasConstantSeed() const { return _hasConstantSeed; }
- int getConstantSeed() const { return _seed; }
- int getUnspecifiedSeed();
-
-protected:
- PROGRAM_TYPE _program;
-
- class FileEntryType {
- public:
- FileEntryType(const QuickString &filename, ContextFileType fileType, ContextRecordType recordType)
- : _fileName(filename), _fileType(fileType), _recordType(recordType) {}
- QuickString _fileName;
- ContextFileType _fileType;
- ContextRecordType _recordType;
- };
- vector<FileEntryType> _inputFiles;
- map<QuickString, PROGRAM_TYPE> _programNames;
-
- bool _useMergedIntervals;
- NewGenomeFile *_genomeFile;
-
- ContextFileType _outputFileType;
- bool _outputTypeDetermined;
-
- map<int, QuickString> _headers;
- map<int, BamTools::RefVector> _references;
-
- QuickString _errorMsg;
- vector<bool> _argsProcessed; //used for processing cmdLine args.
- int _argc;
- char **_argv;
- int _skipFirstArgs;
- bool _showHelp;
- bool _obeySplits;
- bool _uncompressedBam;
- bool _useBufferedOutput;
-
- bool _anyHit;
- bool _noHit;
- bool _writeA;
- bool _writeB;
- bool _leftJoin;
- bool _writeCount;
- bool _writeOverlap;
- bool _writeAllOverlap;
- bool _haveFraction;
- float _overlapFraction;
- bool _reciprocal;
- bool _sameStrand;
- bool _diffStrand;
- bool _sortedInput;
- bool _printHeader;
- bool _printable;
- bool _explicitBedOutput;
- int _queryFileIdx;
- int _databaseFileIdx;
- int _bamHeaderAndRefIdx;
- int _maxNumDatabaseFields;
- bool _useFullBamTags;
-
- bool _reportCount;
- int _maxDistance;
- bool _reportNames;
- bool _reportScores;
- QuickString _scoreOp;
- set<QuickString> _validScoreOps;
-
- int _numOutputRecords;
-
- bool _hasConstantSeed;
- int _seed;
- bool _forwardOnly;
- bool _reverseOnly;
-
- void markUsed(int i) { _argsProcessed[i] = true; }
- bool isUsed(int i) const { return _argsProcessed[i]; }
- bool cmdArgsValid();
- bool isValidIntersectState();
- bool isValidSampleState();
-};
-
-#endif /* CONTEXT_H_ */
diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
index 13b0864b9c85cd9a7264c0e42cdcc4f942c975f1..cd30b203881b61bfa81ec85ec6ac069bdceb2640 100644
--- a/src/utils/Contexts/ContextBase.cpp
+++ b/src/utils/Contexts/ContextBase.cpp
@@ -12,6 +12,7 @@
ContextBase::ContextBase()
:
_program(UNSPECIFIED_PROGRAM),
+ _allFilesOpened(false),
_useMergedIntervals(false),
_genomeFile(NULL),
_outputFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
@@ -69,9 +70,14 @@ ContextBase::ContextBase()
ContextBase::~ContextBase()
{
- if (_genomeFile != NULL) {
- delete _genomeFile;
- _genomeFile = NULL;
+ delete _genomeFile;
+ _genomeFile = NULL;
+
+ //close all files and delete FRM objects.
+ for (int i=0; i < (int)_files.size(); i++) {
+ _files[i]->close();
+ delete _files[i];
+ _files[i] = NULL;
}
}
@@ -89,8 +95,8 @@ bool ContextBase::determineOutputType() {
//Otherwise, if there are any BAM files in the input,
//then the output should be BAM.
- for (_i = 0; _i < (int)_inputFiles.size(); _i++) {
- if (_inputFiles[_i]._fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ for (_i = 0; _i < (int)_files.size(); _i++) {
+ if (_files[_i]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
_bamHeaderAndRefIdx = _i;
_outputTypeDetermined = true;
@@ -176,7 +182,16 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
bool ContextBase::isValidState()
{
- return cmdArgsValid();
+ if (!openFiles()) {
+ return false;
+ }
+ if (!cmdArgsValid()) {
+ return false;
+ }
+ if (!determineOutputType()) {
+ return false;
+ }
+ return true;
}
@@ -194,12 +209,36 @@ bool ContextBase::cmdArgsValid()
return retval;
}
+bool ContextBase::openFiles() {
+
+ //Make a vector of FileRecordMgr objects by going through the vector
+ //of filenames and opening each one.
+ if (_allFilesOpened) {
+ return true;
+ }
+ _files.resize(_fileNames.size());
+
+ for (int i = 0; i < (int)_fileNames.size(); i++) {
+ FileRecordMgr *frm = new FileRecordMgr(_fileNames[i], _sortedInput);
+ if (hasGenomeFile()) {
+ frm->setGenomeFile(_genomeFile);
+ }
+ frm->setFullBamFlags(_useFullBamTags);
+ if (!frm->open()) {
+ return false;
+ }
+ _files[i] = frm;
+ }
+ _allFilesOpened = true;
+ return true;
+}
+
int ContextBase::getBamHeaderAndRefIdx() {
if (_bamHeaderAndRefIdx != -1) {
//already found which BAM file to use for the header
return _bamHeaderAndRefIdx;
}
- if (_inputFiles[_queryFileIdx]._fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
+ if (_files[_queryFileIdx]->getFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
_bamHeaderAndRefIdx = _queryFileIdx;
} else {
_bamHeaderAndRefIdx = _databaseFileIdx;
diff --git a/src/utils/Contexts/ContextBase.h b/src/utils/Contexts/ContextBase.h
index 2335f11c6d0e084bfcdd4d7fac82385f27adbafa..872193fd5d8724538abf722e8e22b4cbfdf7efff 100644
--- a/src/utils/Contexts/ContextBase.h
+++ b/src/utils/Contexts/ContextBase.h
@@ -20,6 +20,7 @@
#include "version.h"
#include "BedtoolsTypes.h"
#include "FileRecordTypeChecker.h"
+#include "FileRecordMgr.h"
#include "NewGenomeFile.h"
#include "api/BamReader.h"
#include "api/BamAux.h"
@@ -39,34 +40,20 @@ public:
MULTICOV, TAG, JACCARD, OVERLAP, IGV, LINKS,MAKEWINDOWS, GROUPBY, EXPAND } PROGRAM_TYPE;
PROGRAM_TYPE getProgram() const { return _program; }
+ FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }
void setProgram(PROGRAM_TYPE program) { _program = program; }
- void addInputFile(const QuickString &inputFile,
- ContextFileType explicitFileType = FileRecordTypeChecker::UNKNOWN_FILE_TYPE,
- ContextRecordType explicitRecordType = FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
- _inputFiles.push_back(FileEntryType(inputFile, explicitFileType, explicitRecordType));
- }
-
- int getNumInputFiles() const { return _inputFiles.size(); }
- const QuickString &getInputFileName(int fileNum) const { return _inputFiles[fileNum]._fileName; }
- ContextFileType getInputFileType(int fileNum) const { return _inputFiles[fileNum]._fileType; }
- void setInputFileType(int fileNum, ContextFileType fileType) { _inputFiles[fileNum]._fileType = fileType; }
- ContextRecordType getInputRecordType(int fileNum) const { return _inputFiles[fileNum]._recordType; }
- void setInputRecordType(int fileNum, ContextRecordType recordType) { _inputFiles[fileNum]._recordType = recordType; }
- //HERE ARE SOME SIMPLER VERSIONS OF THE ABOVE FOR APPS THAT HAVE ONLY ONE INPUT FILE
- const QuickString &getInputFileName() const { return _inputFiles[0]._fileName; }
- ContextFileType getInputFileType() const { return _inputFiles[0]._fileType; }
- void setInputFileType(ContextFileType fileType) { _inputFiles[0]._fileType = fileType; }
- ContextRecordType getInputRecordType() const { return _inputFiles[0]._recordType; }
- void setInputRecordType(ContextRecordType recordType) { _inputFiles[0]._recordType = recordType; }
- int getInputFileIdx() const { return 0; }
+ void addInputFile(const QuickString &inputFile) { _fileNames.push_back(inputFile); }
+
+ int getNumInputFiles() const { return _fileNames.size(); }
+ const QuickString &getInputFileName(int fileNum) const { return _fileNames[fileNum]; }
+ ContextFileType getInputFileType(int fileNum) const { return _files[fileNum]->getFileType(); }
+ ContextRecordType getInputRecordType(int fileNum) const { return _files[fileNum]->getRecordType(); }
virtual bool determineOutputType();
- const QuickString &getHeader(int fileIdx) { return _headers[fileIdx]; }
- void setHeader(int fileIdx, const QuickString &header) { _headers[fileIdx] = header; }
- const BamTools::RefVector &getReferences(int fileIdx) { return _references[fileIdx]; }
- void setReferences(int fileIdx, const BamTools::RefVector &refs) { _references[fileIdx] = refs; }
+ const QuickString &getHeader(int fileIdx) { return _files[fileIdx]->getHeader(); }
+ const BamTools::RefVector &getBamReferences(int fileIdx) { return _files[fileIdx]->getBamReferences(); }
int getBamHeaderAndRefIdx(); //return idx of 1st query that is BAM. If none, first DB that is BAM.
bool getUseMergedIntervals() const { return _useMergedIntervals; }
@@ -160,15 +147,9 @@ public:
protected:
PROGRAM_TYPE _program;
- class FileEntryType {
- public:
- FileEntryType(const QuickString &filename, ContextFileType fileType, ContextRecordType recordType)
- : _fileName(filename), _fileType(fileType), _recordType(recordType) {}
- QuickString _fileName;
- ContextFileType _fileType;
- ContextRecordType _recordType;
- };
- vector<FileEntryType> _inputFiles;
+ vector<QuickString> _fileNames;
+ vector<FileRecordMgr *> _files;
+ bool _allFilesOpened;
map<QuickString, PROGRAM_TYPE> _programNames;
bool _useMergedIntervals;
@@ -230,6 +211,7 @@ protected:
void markUsed(int i) { _argsProcessed[i] = true; }
bool isUsed(int i) const { return _argsProcessed[i]; }
bool cmdArgsValid();
+ bool openFiles();
//set cmd line params and counter, i, as members so code
//is more readable (as opposed to passing all 3 everywhere).
diff --git a/src/utils/Contexts/ContextIntersect.cpp b/src/utils/Contexts/ContextIntersect.cpp
index d43994fd4d969235b091aee0dfb7e0d693fbb2dc..fecf51d115ebde0c87446c9341cb95e1cf4b89ea 100644
--- a/src/utils/Contexts/ContextIntersect.cpp
+++ b/src/utils/Contexts/ContextIntersect.cpp
@@ -88,7 +88,7 @@ bool ContextIntersect::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
bool ContextIntersect::isValidState()
{
- if (!cmdArgsValid()) {
+ if (!ContextBase::isValidState()) {
return false;
}
@@ -149,7 +149,7 @@ bool ContextIntersect::isValidState()
if (getAnyHit() || getNoHit() || getWriteCount()) {
setPrintable(false);
}
- if (_inputFiles.size() < 2 ) {
+ if (_files.size() != 2 ) {
return false;
}
return true;
@@ -159,6 +159,15 @@ bool ContextIntersect::determineOutputType() {
if (_outputTypeDetermined) {
return true;
}
+
+ //determine the maximum number of database fields.
+ for (int i=0; i < (int)_files.size(); i++) {
+ int numFields = _files[i]->getNumFields();
+ if ( numFields > _maxNumDatabaseFields) {
+ _maxNumDatabaseFields = numFields;
+ }
+ }
+
//If the query is BAM, and bed output wasn't specified, then the output is BAM.
if (getQueryFileType() == FileRecordTypeChecker::BAM_FILE_TYPE && !getExplicitBedOutput()) {
setOutputFileType(FileRecordTypeChecker::BAM_FILE_TYPE);
@@ -196,7 +205,6 @@ bool ContextIntersect::handle_abam()
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
- setInputFileType(_queryFileIdx, FileRecordTypeChecker::BAM_FILE_TYPE);
return true;
}
diff --git a/src/utils/Contexts/ContextIntersect.h b/src/utils/Contexts/ContextIntersect.h
index 9449845125d43a6a8c904d4061580675ccaf34f2..0144a1210eef34278c19ac9fe529fd74db9ccfe6 100644
--- a/src/utils/Contexts/ContextIntersect.h
+++ b/src/utils/Contexts/ContextIntersect.h
@@ -25,12 +25,12 @@ public:
void setQueryFileIdx(int idx) { _queryFileIdx = idx; }
int getDatabaseFileIdx() const { return _databaseFileIdx; }
void setDatabaseFileIdx(int idx) { _databaseFileIdx = idx; }
- const QuickString &getQueryFileName() const { return _inputFiles[_queryFileIdx]._fileName; }
- const QuickString &getDatabaseFileName() const { return _inputFiles[_databaseFileIdx]._fileName; }
- ContextFileType getQueryFileType() const { return _inputFiles[_queryFileIdx]._fileType; }
- ContextFileType getDatabaseFileType() const { return _inputFiles[_databaseFileIdx]._fileType; }
- ContextRecordType getQueryRecordType() const { return _inputFiles[_queryFileIdx]._recordType; }
- ContextRecordType getDatabaseRecordType() const { return _inputFiles[_databaseFileIdx]._recordType; }
+ const QuickString &getQueryFileName() const { return _files[_queryFileIdx]->getFileName(); }
+ const QuickString &getDatabaseFileName() const { return _files[_databaseFileIdx]->getFileName(); }
+ ContextFileType getQueryFileType() const { return _files[_queryFileIdx]->getFileType(); }
+ ContextFileType getDatabaseFileType() const { return _files[_databaseFileIdx]->getFileType(); }
+ ContextRecordType getQueryRecordType() const { return _files[_queryFileIdx]->getRecordType(); }
+ ContextRecordType getDatabaseRecordType() const { return _files[_databaseFileIdx]->getRecordType(); }
int getMaxNumDatabaseFields() const { return _maxNumDatabaseFields; }
void setMaxNumDatabaseFields(int val) { _maxNumDatabaseFields = val; }
diff --git a/src/utils/Contexts/ContextMap.cpp b/src/utils/Contexts/ContextMap.cpp
index 80fd2b7bda0b485752223951d3906a4f0bde5ed8..d94d08884aa1c3e2caef93939b84179b6332ff80 100644
--- a/src/utils/Contexts/ContextMap.cpp
+++ b/src/utils/Contexts/ContextMap.cpp
@@ -60,12 +60,10 @@ bool ContextMap::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
bool ContextMap::isValidState()
{
- if (!cmdArgsValid()) {
+ if (!ContextIntersect::isValidState()) {
return false;
}
- ContextIntersect::isValidState();
-
if (getDatabaseFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
//throw Error
cerr << endl << "*****"
@@ -76,8 +74,7 @@ bool ContextMap::isValidState()
}
// TODO
// enforce any specific checks for Map.
-
- return ContextIntersect::isValidState();
+ return true;
}
diff --git a/src/utils/Contexts/ContextSample.cpp b/src/utils/Contexts/ContextSample.cpp
index 452b1f8ae33923e40062d3459564909880d8a872..38fbcb3c9fc47512bd7078841424c63bf4b269f9 100644
--- a/src/utils/Contexts/ContextSample.cpp
+++ b/src/utils/Contexts/ContextSample.cpp
@@ -43,10 +43,10 @@ bool ContextSample::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
bool ContextSample::isValidState()
{
- if (!cmdArgsValid()) {
+ if (!ContextBase::isValidState()) {
return false;
}
- if (_inputFiles.size() != 1) {
+ if (_files.size() != 1) {
_errorMsg = "\n***** ERROR: input file not specified. *****";
// Allow one and only input file for now
return false;
diff --git a/src/utils/Contexts/Makefile b/src/utils/Contexts/Makefile
index 8746fcdd9f83dc4c63ffd29a381fdaa6ccddb5ca..7ddc3c6c3cac4427c0578a33bc6822636bdb8a73 100644
--- a/src/utils/Contexts/Makefile
+++ b/src/utils/Contexts/Makefile
@@ -6,9 +6,12 @@ UTILITIES_DIR = ../../utils/
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/fileType/ \
- -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
-I$(UTILITIES_DIR)/GenomeFile/ \
- -I$(UTILITIES_DIR)/BamTools/include/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
diff --git a/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp b/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
index a9d129d75f9fb3904ef4f7e06b0211842d2607a9..ab717f921236e17c8610e683a91c843b628c1736 100644
--- a/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
@@ -4,44 +4,17 @@
BamFileReader::BamFileReader()
: _bamReader(NULL),
_eof(false),
- _useTags(true),
- _shouldDeleteBamReader(false)
+ _useTags(true)
{
}
BamFileReader::~BamFileReader()
{
- if (_bamReader != NULL && _shouldDeleteBamReader) {
- delete _bamReader;
- _shouldDeleteBamReader = false;
- _bamReader = NULL;
- }
}
bool BamFileReader::open()
{
-// if (_bamReader == NULL) {
-// _bamReader = new BamTools::BamReader();
-// _shouldDeleteBamReader = true;
-// }
-// if (_inputStream != NULL) {
-// try {
-// _bamReader->OpenStream(_inputStream);
-// }
-// catch (...) {
-// fprintf(stderr, "ERROR: Unable to open BAM file from standard input.\n");
-// exit(1);
-// }
-// } else {
-// try {
-// _bamReader->Open(_filename);
-// }
-// catch (...) {
-// fprintf(stderr, "ERROR: Unable to open BAM file %s\n", _filename.c_str());
-// exit(1);
-// }
-// }
_bamHeader = _bamReader->GetHeaderText();
_references = _bamReader->GetReferenceData();
diff --git a/src/utils/FileRecordTools/FileReaders/BamFileReader.h b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
index deb03a2986f1bee63d32999435dc9807b239294e..8bea945ed8b1bdbecfaec9e8e20d82bf6e26f295 100644
--- a/src/utils/FileRecordTools/FileReaders/BamFileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
@@ -48,17 +48,18 @@ public:
void getName(QuickString &) const;
void getScore(QuickString &) const;
char getStrand() const;
+ virtual int getNumFields() const { return MINIMUM_PRINTABLE_BAM_FIELDS; }
protected:
+
BamTools::BamReader *_bamReader;
BamTools::BamAlignment _bamAlignment;
bool _eof;
QuickString _bamHeader;
BamTools::RefVector _references;
bool _useTags;
- bool _shouldDeleteBamReader;
-
+ static const int MINIMUM_PRINTABLE_BAM_FIELDS = 6;
void extractNameFromCore();
};
diff --git a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
index 55ec8865e0745c90f7d80a5b93b48b07d0f4fc74..27f07894c347c2b871201f933287ed410c555bd0 100644
--- a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
+++ b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
@@ -26,13 +26,11 @@ BufferedStreamMgr::BufferedStreamMgr(const QuickString &filename)
BufferedStreamMgr::~BufferedStreamMgr()
{
- if (_mainBuf != NULL) {
- delete [] _mainBuf;
- }
- if (_inputStreamMgr != NULL) {
- delete _inputStreamMgr;
- _inputStreamMgr = NULL;
- }
+ delete [] _mainBuf;
+ _mainBuf = NULL;
+
+ delete _inputStreamMgr;
+ _inputStreamMgr = NULL;
}
bool BufferedStreamMgr::init()
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.h b/src/utils/FileRecordTools/FileReaders/FileReader.h
index f8d25d0da81c69f513ea242dff209099f9e199cb..29c25630918e27408fb6e099549781a94d97cf47 100644
--- a/src/utils/FileRecordTools/FileReaders/FileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.h
@@ -29,6 +29,7 @@ public:
virtual int getCurrChromdId() const { return _currChromId; }
virtual bool hasHeader() const = 0;
virtual const QuickString &getHeader() const =0;
+ virtual int getNumFields() const = 0;
protected:
string _filename;
BufferedStreamMgr *_bufStreamMgr;
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
index 5b1d0a9c10831dcfc123efe560ec86acf4fbac3b..2035b9c6529e8ac97f53766b22c2fd98c8eba56b 100644
--- a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
@@ -35,38 +35,29 @@ InputStreamMgr::InputStreamMgr(const QuickString &filename, bool buildScanBuffer
InputStreamMgr::~InputStreamMgr() {
- if (_pushBackStreamBuf != NULL) {
- delete _pushBackStreamBuf;
- _pushBackStreamBuf = NULL;
- }
- if (_inputFileStream != NULL) {
- delete _inputFileStream;
- _inputFileStream = NULL;
- }
- if (_oldInputStream != NULL) {
- delete _oldInputStream;
- _oldInputStream = NULL;
- }
- if (_infStreamBuf != NULL) {
- delete _infStreamBuf;
- _infStreamBuf = NULL;
- }
- if (_bamReader != NULL) {
- delete _bamReader;
- _bgStream = NULL;
- }
- if (_bgStream != NULL) {
- delete _bgStream;
- _bgStream = NULL;
- }
- if (_finalInputStream != NULL) {
- delete _finalInputStream;
- _finalInputStream = NULL;
- }
- if (_tmpZipBuf != NULL) {
- delete [] _tmpZipBuf;
- _tmpZipBuf = NULL;
- }
+ delete _pushBackStreamBuf;
+ _pushBackStreamBuf = NULL;
+
+ delete _inputFileStream;
+ _inputFileStream = NULL;
+
+ delete _oldInputStream;
+ _oldInputStream = NULL;
+
+ delete _infStreamBuf;
+ _infStreamBuf = NULL;
+
+ delete _bamReader;
+ _bgStream = NULL;
+
+ delete _bgStream;
+ _bgStream = NULL;
+
+ delete _finalInputStream;
+ _finalInputStream = NULL;
+
+ delete [] _tmpZipBuf;
+ _tmpZipBuf = NULL;
}
bool InputStreamMgr::init()
@@ -98,7 +89,6 @@ bool InputStreamMgr::init()
//now we have a PushBackStreamBuf. Make a new stream.
_finalInputStream = new istream(_pushBackStreamBuf);
populateScanBuffer();
-// resetStream();
return true;
}
@@ -240,9 +230,7 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
_bamRuledOut = true;
_numBytesInBuffer = 0;
_infStreamBuf = new InflateStreamBuf(_finalInputStream);
- if (_oldInputStream != NULL) {
- delete _oldInputStream;
- }
+ delete _oldInputStream;
_oldInputStream = _finalInputStream;
_finalInputStream = new istream(_infStreamBuf);
return false;
@@ -251,23 +239,6 @@ bool InputStreamMgr::detectBamOrBgzip(int &numChars, int currChar)
return false;
}
-//void InputStreamMgr::decompressBuffer()
-//{
-// //allocate an array to hold uncompressed data.
-// _saveDataStr.clear();
-// uInt maxDecompressSize = 20 * _numBytesInBuffer;
-// unsigned char *newScanBuffer = new unsigned char[maxDecompressSize];
-// memset(newScanBuffer, 0, maxDecompressSize);
-//
-// unsigned int numDecompressChars = inflateGzippedArray(_scanBuffer, newScanBuffer, maxDecompressSize, _numBytesInBuffer);
-//
-// // newScanBuffer should now contain uncompressed data.
-// //delete old buffer, point it at new buffer.
-// _saveDataStr.append((char *)newScanBuffer, numDecompressChars);
-//
-// delete [] newScanBuffer;
-//}
-
void InputStreamMgr::readZipChunk()
{
if (_tmpZipBuf == NULL) {
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
index 12739abe41b42c9412c989387e846cd5464eaf01..38074edf3513817e7413cf4426269fe618d84b7d 100644
--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
@@ -16,6 +16,7 @@ SingleLineDelimTextFileReader::SingleLineDelimTextFileReader(int numFields, char
SingleLineDelimTextFileReader::~SingleLineDelimTextFileReader()
{
delete [] _delimPositions;
+ _delimPositions = NULL;
}
bool SingleLineDelimTextFileReader::readEntry()
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index 16ebf006d9eac5054940b4147e18833f6e66ff1e..38fc056b483236611748943ebcce4a7228f0a95f 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -1,50 +1,47 @@
#include "FileRecordMgr.h"
-#include "ContextIntersect.h"
#include "FreeList.h"
#include "Record.h"
+#include "NewGenomeFile.h"
-FileRecordMgr::FileRecordMgr(int fileIdx, ContextBase *context)
+FileRecordMgr::FileRecordMgr(const QuickString &filename, bool isSorted)
:
+ _filename(filename),
_bufStreamMgr(NULL),
- _contextFileIdx(fileIdx),
- _context(context),
_fileReader(NULL),
_fileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
_recordType(FileRecordTypeChecker::UNKNOWN_RECORD_TYPE),
_recordMgr(NULL),
+ _isSortedInput(isSorted),
_freeListBlockSize(512),
_useFullBamTags(false),
- _headerSet(false),
_prevStart(INT_MAX),
_prevChromId(-1),
_mustBeForward(false),
_mustBeReverse(false),
_totalRecordLength(0),
- _totalMergedRecordLength(0)
+ _totalMergedRecordLength(0),
+ _blockMgr(NULL),
+ _bamReader(NULL),
+ _hasGenomeFile(false),
+ _genomeFile(NULL)
{
}
FileRecordMgr::~FileRecordMgr(){
- if (_bufStreamMgr != NULL) {
- delete _bufStreamMgr;
- _bufStreamMgr = NULL;
- }
- if (_fileReader != NULL) {
- close(); //just make sure file was closed.
- delete _fileReader;
- _fileReader = NULL;
- }
- if (_recordMgr != NULL) {
- delete _recordMgr;
- _recordMgr = NULL;
- }
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+
+ close(); //just make sure file was closed.
+ delete _fileReader;
+ _fileReader = NULL;
+
+ delete _recordMgr;
+ _recordMgr = NULL;
}
bool FileRecordMgr::open(){
-
- _filename = _context->getInputFileName(_contextFileIdx);
_bufStreamMgr = new BufferedStreamMgr(_filename);
if (!_bufStreamMgr->init()) {
cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
@@ -72,31 +69,14 @@ bool FileRecordMgr::open(){
_bufStreamMgr = NULL;
exit(1);
}
- _context->setInputFileType(_contextFileIdx, _fileType);
- _context->setInputRecordType(_contextFileIdx, _recordType);
-
- //if this is a database file, and the numFields is greater than the numFields in other DB files, update.
- // TBD: This is one of many things that will need to be changed to support multiple database files in future versions.
- int numFields = _bufStreamMgr->getTypeChecker().getNumFields();
- if (_context->hasIntersectMethods()) {
- if (_contextFileIdx == (static_cast<ContextIntersect *>(_context))->getDatabaseFileIdx() && numFields >
- (static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields()) {
- (static_cast<ContextIntersect *>(_context))->setMaxNumDatabaseFields(numFields);
- }
- }
- if (_fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
- _context->setHeader(_contextFileIdx, _fileReader->getHeader());
- _context->setReferences(_contextFileIdx, static_cast<BamFileReader *>(_fileReader)->getReferences());
- _headerSet = true;
- }
+
return true;
}
void FileRecordMgr::close(){
- if (_bufStreamMgr != NULL) {
- delete _bufStreamMgr;
- _bufStreamMgr = NULL;
- }
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+
if (_fileReader != NULL) {
_fileReader->close();
delete _fileReader;
@@ -106,7 +86,6 @@ void FileRecordMgr::close(){
bool FileRecordMgr::eof(){
return _fileReader->eof();
-// return _storedRecords.empty() && _fileReader->eof() ? true: false;
}
Record *FileRecordMgr::allocateAndGetNextRecord()
@@ -117,10 +96,6 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
if (!_fileReader->readEntry()) {
return NULL;
}
- if (!_headerSet && _fileReader->hasHeader()) {
- _context->setHeader(_contextFileIdx, _fileReader->getHeader());
- _headerSet = true;
- }
Record *record = NULL;
record = _recordMgr->allocateRecord();
if (!record->initFromFile(_fileReader)) {
@@ -128,17 +103,18 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
return NULL;
}
- // In the rare case of Bam records where both the read and it's mate failed to map,
- // Ignore the record. Delete and return null.
+ // If the record is unmapped, don't test for valid coords or sort order,
+ // but still return it so the -v (noHit) option and the like will still
+ // see it.
- if (!(record->isUnmapped() )) {
+ if (!record->isUnmapped()) {
if (!record->coordsValid()) {
cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
exit(1);
}
//test for sorted order, if necessary.
- if (_context->getSortedInput()) {
+ if (_isSortedInput) {
testInputSortOrder(record);
}
}
@@ -149,8 +125,8 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
void FileRecordMgr::assignChromId(Record *record) {
const QuickString &currChrom = record->getChrName();
- if (currChrom != _prevChrom && _context->hasGenomeFile()) {
- _prevChromId = _context->getGenomeFile()->getChromId(currChrom);
+ if (currChrom != _prevChrom && _hasGenomeFile) {
+ _prevChromId = _genomeFile->getChromId(currChrom);
record->setChromId(_prevChromId);
} else {
record->setChromId(_prevChromId);
@@ -185,8 +161,8 @@ void FileRecordMgr::testInputSortOrder(Record *record)
} else {
//new chrom has not been seen before.
//TBD: test genome file for ChromId.
- if (_context->hasGenomeFile()) {
- int currChromId = _context->getGenomeFile()->getChromId(currChrom);
+ if (_hasGenomeFile) {
+ int currChromId = _genomeFile->getChromId(currChrom);
if (currChromId < _prevChromId) {
sortError(record, true);
} else {
@@ -209,7 +185,7 @@ void FileRecordMgr::sortError(const Record *record, bool genomeFileError)
{
if (genomeFileError) {
cerr << "Error: Sorted input specified, but the file " << _filename << " has the following record with a different sort order than the genomeFile " <<
- _context->getGenomeFile()->getGenomeFileName() << endl;
+ _genomeFile->getGenomeFileName() << endl;
} else {
cerr << "Error: Sorted input specified, but the file " << _filename << " has the following out of order record" << endl;
}
@@ -232,7 +208,7 @@ void FileRecordMgr::allocateFileReader()
case FileRecordTypeChecker::BAM_FILE_TYPE:
_fileReader = new BamFileReader();
- (static_cast<BamFileReader *>(_fileReader))->setUseTags(_context->getUseFullBamTags());
+ (static_cast<BamFileReader *>(_fileReader))->setUseTags(_useFullBamTags);
(static_cast<BamFileReader *>(_fileReader))->setBamReader(_bufStreamMgr->getBamReader());
break;
default:
@@ -240,6 +216,14 @@ void FileRecordMgr::allocateFileReader()
}
}
+const BamTools::RefVector & FileRecordMgr::getBamReferences() {
+ // exta safety check to insure user checked the file type first.
+ if (_fileType != FileRecordTypeChecker::BAM_FILE_TYPE) {
+ cerr << "Error: Attempted to get BAM references from file " << _filename << ", which is NOT a BAM file." << endl;
+ exit(1);
+ }
+ return static_cast<BamFileReader *>(_fileReader)->getReferences();
+}
#ifdef false
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
index ff523c47547b8e84d0b166539f9f6cedbd79e937..b4e76e92f1e7e1618d67d28dcedba1581862024c 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -16,7 +16,6 @@ using namespace std;
//#include "DualQueue.h"
//include headers for all FileReader and derivative classes.
-#include "ContextBase.h"
#include "BufferedStreamMgr.h"
#include "FileReader.h"
#include "SingleLineDelimTextFileReader.h"
@@ -29,50 +28,47 @@ using namespace std;
#include "BlockMgr.h"
class Record;
+class NewGenomeFile;
+
class FileRecordMgr {
public:
- FileRecordMgr(int inputFileIdx, ContextBase *context);
+ FileRecordMgr(const QuickString & filename, bool isSorted = false);
~FileRecordMgr();
bool open();
void close();
bool eof();
- //NOTE: FOR Non-BAM FILES, HEADER INFORMATION IS CURRENTLY ONLY AVAILABLE AFTER 1st CALL
- //TO allocateAndGetNextRecord().
+ const QuickString &getFileName() const { return _filename;}
bool hasHeader() const { return _fileReader->hasHeader(); }
const QuickString &getHeader() const { return _fileReader->getHeader(); }
bool recordsHaveName() const {
- testBufferedMgr();
return _bufStreamMgr->getTypeChecker().recordTypeHasName(_recordType);
}
bool recordsHaveScore() const {
- testBufferedMgr();
return _bufStreamMgr->getTypeChecker().recordTypeHasScore(_recordType);
}
bool recordsHaveStrand() const {
- testBufferedMgr();
return _bufStreamMgr->getTypeChecker().recordTypeHasStrand(_recordType);
}
FileRecordTypeChecker::FILE_TYPE getFileType() const {
- testBufferedMgr();
return _fileType;
}
FileRecordTypeChecker::RECORD_TYPE getRecordType() const {
- testBufferedMgr();
return _recordType;
}
const string &getFileTypeName() const {
- testBufferedMgr();
return _bufStreamMgr->getTypeChecker().getFileTypeName();
}
const string &getRecordTypeName() const {
- testBufferedMgr();
return _bufStreamMgr->getTypeChecker().getRecordTypeName();
}
+ const BamTools::RefVector &getBamReferences();
+
+ int getNumFields() const { return _fileReader->getNumFields(); }
//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!
@@ -139,20 +135,22 @@ public:
//will use all the tags, if more information is desired.
//MUST BE CALLED BEFORE THE BAM FILE IS OPEN.
void setFullBamFlags(bool flag) { _useFullBamTags = flag; }
+ void setGenomeFile(NewGenomeFile *genomeFile) {
+ _genomeFile = genomeFile;
+ _hasGenomeFile = true;
+ }
private:
QuickString _filename;
BufferedStreamMgr *_bufStreamMgr;
- int _contextFileIdx;
- ContextBase *_context;
FileReader *_fileReader;
FileRecordTypeChecker::FILE_TYPE _fileType;
FileRecordTypeChecker::RECORD_TYPE _recordType;
RecordMgr *_recordMgr;
+ bool _isSortedInput;
int _freeListBlockSize;
bool _useFullBamTags;
- bool _headerSet;
//members for enforcing sorted order.
set<QuickString> _foundChroms;
@@ -172,18 +170,14 @@ private:
BlockMgr *_blockMgr;
BamTools::BamReader *_bamReader;
-
+ bool _hasGenomeFile;
+ NewGenomeFile *_genomeFile;
void allocateFileReader();
void testInputSortOrder(Record *record);
void assignChromId(Record *);
void sortError(const Record *record, bool genomeFileError);
- void testBufferedMgr() const {
- if (_bufStreamMgr == NULL) {
- cerr << "Error: attempted to access type information for file " << _context->getInputFileName(_contextFileIdx) << " before it was opened." << endl;
- exit (1);
- }
- }
+
#ifdef false
void deleteAllMergedItemsButKey(RecordKeyList &recList);
diff --git a/src/utils/FileRecordTools/Makefile b/src/utils/FileRecordTools/Makefile
index cacf887f920b03582030d3041be93fbacacf88b8..9d021179772c29991565b157bb9aba7d0063e40f 100644
--- a/src/utils/FileRecordTools/Makefile
+++ b/src/utils/FileRecordTools/Makefile
@@ -9,8 +9,7 @@ INCLUDES = -I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
-I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/general/ \
- -I$(UTILITIES_DIR)/Contexts/ \
- -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
@@ -22,7 +21,7 @@ SUBDIRS = ./FileReaders \
# ----------------------------------
# define our source and object files
# ----------------------------------
-SOURCES= FileRecordMgr.cpp FileRecordMgr.h RecordOutputMgr.cpp RecordOutputMgr.h
+SOURCES= FileRecordMgr.cpp FileRecordMgr.h
OBJECTS= FileRecordMgr.o RecordOutputMgr.o
_EXT_OBJECTS=SingleLineDelimTextFileReader.o BamFileReader.o Bed3Interval.o Bed6Interval.o BedPlusInterval.o Bed12Interval.o BamRecord.o \
SingleLineDelimTransferBuffer.o FileRecordTypeChecker.o QuickString.o ParseTools.o RecordKeyList.o BufferedStreamMgr.o
@@ -32,8 +31,6 @@ BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES) $(SUBDIRS)
@echo " * compiling FileRecordMgr.cpp"
@$(CXX) -c -o $(OBJ_DIR)/FileRecordMgr.o FileRecordMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
- @echo " * compiling RecordOutputMgr.cpp"
- @$(CXX) -c -o $(OBJ_DIR)/RecordOutputMgr.o RecordOutputMgr.cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
@@ -49,7 +46,6 @@ clean:
@rm -f $(OBJ_DIR)/FileRecordTypeChecker.o
@rm -f $(OBJ_DIR)/SingleLineDelimTextFileReader.o
@rm -f $(OBJ_DIR)/SingleLineDelimTransferBuffer.o
- @rm -f $(OBJ_DIR)/RecordOutputMgr.o
.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.cpp b/src/utils/FileRecordTools/Records/BlockMgr.cpp
index 4aede83d0de63f3259cf81e66d20fa59b7c18f05..21b060df73b71af677bde159f1a980c73b48bbf8 100644
--- a/src/utils/FileRecordTools/Records/BlockMgr.cpp
+++ b/src/utils/FileRecordTools/Records/BlockMgr.cpp
@@ -7,17 +7,18 @@
#include "BlockMgr.h"
#include "RecordMgr.h"
-#include "ContextIntersect.h"
#include "Bed12Interval.h"
#include "BamRecord.h"
#include "ParseTools.h"
#include "api/BamAlignment.h"
#include "api/BamAux.h"
-BlockMgr::BlockMgr()
+BlockMgr::BlockMgr(float overlapFraction, bool hasReciprocal)
: _blockRecordsMgr(NULL),
_breakOnDeletionOps(false),
- _breakOnSkipOps(true)
+ _breakOnSkipOps(true),
+ _overlapFraction(overlapFraction),
+ _hasReciprocal(hasReciprocal)
{
_blockRecordsMgr = new RecordMgr(_blockRecordsType);
}
@@ -194,11 +195,11 @@ int BlockMgr::findBlockedOverlaps(RecordKeyList &keyList, RecordKeyList &hitList
}
_overlapBases.push_back(totalHitOverlap);
if (hitHasOverlap) {
- if ((float) totalHitOverlap / (float)keyBlocksSumLength > _context->getOverlapFraction()) {
- if (_context->getReciprocal() &&
- ((float)totalHitOverlap / (float)hitBlockSumLength > _context->getOverlapFraction())) {
+ if ((float) totalHitOverlap / (float)keyBlocksSumLength > _overlapFraction) {
+ if (_hasReciprocal &&
+ ((float)totalHitOverlap / (float)hitBlockSumLength > _overlapFraction)) {
resultList.push_back(hitListIter->value());
- } else if (!_context->getReciprocal()) {
+ } else if (!_hasReciprocal) {
resultList.push_back(hitListIter->value());
}
}
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.h b/src/utils/FileRecordTools/Records/BlockMgr.h
index 86ddfd7e2b5e1b3d7de129e10b18d87b0cb13866..c83b1e0125284bb5743c95ff5d3cc91708a06d04 100644
--- a/src/utils/FileRecordTools/Records/BlockMgr.h
+++ b/src/utils/FileRecordTools/Records/BlockMgr.h
@@ -16,14 +16,12 @@ using namespace std;
#include "FileRecordTypeChecker.h"
#include "RecordKeyList.h"
-class ContextIntersect;
class RecordMgr;
class BlockMgr {
public:
- BlockMgr();
+ BlockMgr(float overlapFraction = 1E-9, bool hasReciprocal = false);
~BlockMgr();
- void setContext(ContextIntersect *context) { _context = context; }
// Return value is the number of blocks this main record has been split into.
void getBlocks(RecordKeyList &keyList, bool &mustDelete);
@@ -46,11 +44,13 @@ public:
private:
RecordMgr *_blockRecordsMgr;
- ContextIntersect *_context;
bool _breakOnDeletionOps;
bool _breakOnSkipOps;
vector<int> _overlapBases;
+ float _overlapFraction;
+ bool _hasReciprocal;
+
// 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);
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index a6b5d18049e71cb0a99625496ab5deed9fb24f0c..5e6045be625799cca515ac056e9a17b33f1908a6 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -37,18 +37,9 @@ bool NewChromSweep::init() {
//Open them, and get the first record from each.
//if any of that goes wrong, return false;
//otherwise, return true.
- _queryFRM = new FileRecordMgr(_context->getQueryFileIdx(), _context);
- _databaseFRM = new FileRecordMgr(_context->getDatabaseFileIdx(), _context);
+ _queryFRM = _context->getFile(_context->getQueryFileIdx());
+ _databaseFRM = _context->getFile(_context->getDatabaseFileIdx());
- if (!_queryFRM->open()) {
- return false;
- }
- if (!_databaseFRM->open()) {
- return false;
- }
-
- _context->determineOutputType();
-
nextRecord(false);
if (_currDatabaseRec == NULL) {
return false;
@@ -77,18 +68,14 @@ NewChromSweep::~NewChromSweep(void) {
if (!_wasInitialized) {
return;
}
- if (_currQueryRec != NULL) {
- _queryFRM->deleteRecord(_currQueryRec);
- }
- if (_currDatabaseRec != NULL) {
- _databaseFRM->deleteRecord(_currDatabaseRec);
- }
- _queryFRM->close();
- _databaseFRM->close();
+ _queryFRM->deleteRecord(_currQueryRec);
+ _currQueryRec = NULL;
- delete _queryFRM;
- delete _databaseFRM;
+ _databaseFRM->deleteRecord(_currDatabaseRec);
+ _currDatabaseRec = NULL;
+ _queryFRM->close();
+ _databaseFRM->close();
}
diff --git a/src/utils/RecordOutputMgr/Makefile b/src/utils/RecordOutputMgr/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..2d196ec11518d10b6f57877c77bc35b7b9063446
--- /dev/null
+++ b/src/utils/RecordOutputMgr/Makefile
@@ -0,0 +1,39 @@
+OBJ_DIR = ../../../obj/
+BIN_DIR = ../../../bin/
+UTILITIES_DIR = ../../utils/
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/general/ \
+ -I$(UTILITIES_DIR)/fileType/ \
+ -I$(UTILITIES_DIR)/Contexts/ \
+ -I$(UTILITIES_DIR)/GenomeFile/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
+ -I$(UTILITIES_DIR)/FileRecordTools/Records/ \
+ -I$(UTILITIES_DIR)/BamTools/include \
+ -I$(UTILITIES_DIR)/BamTools/src/ \
+ -I$(UTILITIES_DIR)/version/
+
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= RecordOutputMgr.cpp RecordOutputMgr.h
+OBJECTS= RecordOutputMgr.o
+_EXT_OBJECTS=
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+
+$(BUILT_OBJECTS): $(SOURCES)
+ @echo " * compiling" $(*F).cpp
+ @$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+ @$(MAKE) --no-print-directory -C $(INCLUDES)
+
+clean:
+ @echo "Cleaning up."
+ @rm -f $(OBJ_DIR)/RecordOutputMgr.o
+
+.PHONY: clean
\ No newline at end of file
diff --git a/src/utils/FileRecordTools/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
similarity index 93%
rename from src/utils/FileRecordTools/RecordOutputMgr.cpp
rename to src/utils/RecordOutputMgr/RecordOutputMgr.cpp
index 29148a2862094f716b519f712af90b7f221a3e8d..55cb70ec9aa74af58b33e5faf32d18b19c0b0bae 100644
--- a/src/utils/FileRecordTools/RecordOutputMgr.cpp
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -50,14 +50,15 @@ RecordOutputMgr::~RecordOutputMgr()
}
-bool RecordOutputMgr::init(ContextBase *context) {
+void RecordOutputMgr::init(ContextBase *context) {
_context = context;
if (_context->getOutputFileType() == FileRecordTypeChecker::BAM_FILE_TYPE) {
//set-up BAM writer.
_bamWriter = new BamTools::BamWriter();
_bamWriter->SetCompressionMode(_context->getUncompressedBam() ? BamTools::BamWriter::Uncompressed : BamTools::BamWriter::Compressed);
- _bamWriter->Open("stdout", _context->getHeader(_context->getBamHeaderAndRefIdx()).c_str(), _context->getReferences(_context->getBamHeaderAndRefIdx()));
+ int bamFileIdx = _context->getBamHeaderAndRefIdx();
+ _bamWriter->Open("stdout", _context->getFile(bamFileIdx)->getHeader().c_str(), _context->getFile(bamFileIdx)->getBamReferences());
} else {
//for everything but BAM, we'll copy output to an output buffer before printing.
_outBuf.reserve(MAX_OUTBUF_SIZE);
@@ -68,14 +69,8 @@ bool RecordOutputMgr::init(ContextBase *context) {
_printable = false;
}
}
- return true;
}
-//void RecordOutputMgr::printHeader(const string &header)
-//{
-// _outBuf.append(header);
-//}
-
bool RecordOutputMgr::printKeyAndTerminate(RecordKeyList &keyList) {
printBamType bamCode = printBamRecord(keyList);
if (bamCode == BAM_AS_BAM) {
@@ -215,15 +210,13 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
}
void RecordOutputMgr::checkForHeader() {
- if (_context->getProgram() == ContextBase::INTERSECT ||
- _context->getProgram() == ContextBase::MAP) {
- if (_context->getPrintHeader()) {
- _outBuf.append(_context->getHeader((static_cast<ContextIntersect *>(_context))->getQueryFileIdx()));
- }
- } else if (_context->getProgram() == ContextBase::SAMPLE) {
- if (_context->getPrintHeader()) {
- _outBuf.append(_context->getHeader(_context->getInputFileIdx()));
- }
+ //if the program is based on intersection, we want the header from the query file.
+ if (_context->hasIntersectMethods()) {
+ int queryIdx = (static_cast<ContextIntersect *>(_context))->getQueryFileIdx();
+ const QuickString &header = _context->getFile(queryIdx)->getHeader();
+ _outBuf.append(header);
+ } else {
+ _outBuf.append(_context->getFile(0)->getHeader());
}
_context->setPrintHeader(false);
if (needsFlush()) flush();
@@ -358,14 +351,14 @@ void RecordOutputMgr::reportOverlapSummary(RecordKeyList &keyList)
void RecordOutputMgr::null(bool queryType, bool dbType)
{
FileRecordTypeChecker::RECORD_TYPE recordType = FileRecordTypeChecker::UNKNOWN_RECORD_TYPE;
- if (_context->getProgram() == ContextBase::INTERSECT) {
+ if (_context->hasIntersectMethods()) {
if (queryType) {
recordType = (static_cast<ContextIntersect *>(_context))->getQueryRecordType();
} else if (dbType) {
recordType = (static_cast<ContextIntersect *>(_context))->getDatabaseRecordType();
}
- } else if (_context->getProgram() == ContextBase::SAMPLE) {
- recordType = _context->getInputRecordType();
+ } else {
+ recordType = _context->getFile(0)->getRecordType();
}
//This is kind of a hack. Need an instance of the correct class of record in order to call it's printNull method.
Record *dummyRecord = NULL;
@@ -434,4 +427,4 @@ void RecordOutputMgr::printKey(const Record *key)
void RecordOutputMgr::flush() {
fwrite(_outBuf.c_str(), 1, _outBuf.size(), stdout);
_outBuf.clear();
-}
\ No newline at end of file
+}
diff --git a/src/utils/FileRecordTools/RecordOutputMgr.h b/src/utils/RecordOutputMgr/RecordOutputMgr.h
similarity index 96%
rename from src/utils/FileRecordTools/RecordOutputMgr.h
rename to src/utils/RecordOutputMgr/RecordOutputMgr.h
index 16b6cb531687d3fd151f41dc67778870537b7d7e..b6296fdadc2d166d4c4d00b0b1f12fe306d46e70 100644
--- a/src/utils/FileRecordTools/RecordOutputMgr.h
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.h
@@ -22,7 +22,7 @@ public:
~RecordOutputMgr();
//The init method must be called after all the input files are open.
- bool init(ContextBase *context);
+ void init(ContextBase *context);
void printRecord(const Record *record);
void printRecord(RecordKeyList &keyList);
@@ -69,4 +69,4 @@ private:
void flush();
};
-#endif /* RECORDOUTPUTMGR_H_ */
\ No newline at end of file
+#endif /* RECORDOUTPUTMGR_H_ */
diff --git a/test/intersect/gdc.gff b/test/intersect/gdc.gff
new file mode 100644
index 0000000000000000000000000000000000000000..4777534dc1f72c874a9b7390ca72fcbb80a1067a
--- /dev/null
+++ b/test/intersect/gdc.gff
@@ -0,0 +1,12 @@
+chr2L . UTR 41 70 0 + . ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
+chr2L . CDS 71 130 0 + . ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
+chr2L . intron 131 170 0 + . ID=mRNA:xs2:intron:131-170;Parent=mRNA:xs2;
+chr2L . CDS 171 200 0 + . ID=mRNA:xs2:CDS:171-200;Parent=mRNA:xs2;
+chr2L . UTR 201 220 0 + . ID=mRNA:xs2:UTR:201-220;Parent=mRNA:xs2;
+chr2L . exon 41 130 0 + . ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
+chr2L . exon 171 220 0 + . ID=mRNA:xs2:exon:171-220;Parent=mRNA:xs2;
+chr2L . mRNA 41 220 0 + . ID=mRNA:xs2;Parent=g2;
+chr2L . CDS 161 230 0 - . ID=tRNA:t2:CDS:161-230;Parent=tRNA:t2;
+chr2L . exon 161 230 0 - . ID=tRNA:t2:exon:161-230;Parent=tRNA:t2;
+chr2L . tRNA 161 230 0 - . ID=tRNA:t2;Parent=t2;
+chr2L . gene 41 220 0 + . ID=g2;
diff --git a/test/intersect/gdc_one.bed b/test/intersect/gdc_one.bed
new file mode 100644
index 0000000000000000000000000000000000000000..377732965e189e333fc7fb578cf21bf151401daa
--- /dev/null
+++ b/test/intersect/gdc_one.bed
@@ -0,0 +1 @@
+chr2L 50 100
diff --git a/test/intersect/new_test-intersect.sh b/test/intersect/new_test-intersect.sh
index 8516c7cb3124956846e8fda2322777593f12eb77..4bdcdf05a1b208d1339dd21c416ef924d59d089e 100755
--- a/test/intersect/new_test-intersect.sh
+++ b/test/intersect/new_test-intersect.sh
@@ -638,8 +638,31 @@ $BT intersect -a gdc.bam -b gdc.bam -bed > obs
check obs gdc_exp
rm obs
+###########################################################
+# Test that if the query is BAM, and bed output is not
+# explicit, and they asked for an output option that is not
+# valid with BAM output, an error is thrown.
+############################################################
+echo " intersect.new.t54...\c"
+echo "***** ERROR: writeAllOverlap option is not valid with BAM query input, unless bed output is specified with -bed option. *****" > exp
+$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
diff --git a/test/map/test-map.sh b/test/map/test-map.sh
index bd25ff4084bcc698b9bb64080b9630c77fb1627e..293d84e3f443ac7b2bbe405e36b77f752c7298f0 100644
--- a/test/map/test-map.sh
+++ b/test/map/test-map.sh
@@ -661,3 +661,24 @@ $BT map -a ivls.bed -b values5.bed -c 0 -o collapse 2> obs
check obs exp
rm obs exp
+
+
+###########################################################
+# Test that Bam database is not allowed
+############################################################
+echo " map.t44...\c"
+echo -e "\n*****\n***** ERROR: BAM database file not currently supported for the map tool." > exp
+$BT map -a ivls.bed -b values.bam 2> obs
+check obs exp
+rm obs exp
+
+
+
+###########################################################
+# Test that -split option works correctly
+############################################################
+echo " map.t45...\c"
+echo "chr1 0 50 three_blocks_match 15 + 0 0 0 3 10,10,10, 0,20,40, ." > exp
+$BT map -o sum -a three_blocks_match.bed -b three_blocks_nomatch.bed -split > obs
+check obs exp
+rm obs exp
diff --git a/test/map/three_blocks_match.bed b/test/map/three_blocks_match.bed
new file mode 100644
index 0000000000000000000000000000000000000000..e4004fae96aaecd82f07dafaf801aa8aee1d3c38
--- /dev/null
+++ b/test/map/three_blocks_match.bed
@@ -0,0 +1 @@
+chr1 0 50 three_blocks_match 15 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/map/three_blocks_nomatch.bed b/test/map/three_blocks_nomatch.bed
new file mode 100644
index 0000000000000000000000000000000000000000..3db90e037111ae9bf754a24e163872c76a431eb2
--- /dev/null
+++ b/test/map/three_blocks_nomatch.bed
@@ -0,0 +1 @@
+chr1 10 60 three_blocks_nomatch 25 + 0 0 0 3 10,10,10, 0,20,40,
diff --git a/test/map/values.bam b/test/map/values.bam
new file mode 100644
index 0000000000000000000000000000000000000000..97caea3c59eed7e599621bcbec98d78441224b59
Binary files /dev/null and b/test/map/values.bam differ
diff --git a/test/map/values.bed b/test/map/values.bed
index 3710f4c7bd6fbd7984f60c32f801591390eefae9..74a08390d2f02e5da58417f197047498553a8003 100644
--- a/test/map/values.bed
+++ b/test/map/values.bed
@@ -5,4 +5,4 @@ chr1 120 130 a4 1 +
chr3 0 10 a5 1 +
chr3 10 20 a6 2 +
chr3 20 30 a7 3 +
-chr3 120 130 a8 4 +
\ No newline at end of file
+chr3 120 130 a8 4 +