diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index 3721f9616e6fff9128fad5c643e9c5b644f6b30c..0657e1ebbdf6ec493759dc2d945d850fdcbc2515 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -44,10 +44,10 @@ FileRecordMgr::~FileRecordMgr(){
bool FileRecordMgr::open(){
- const QuickString &filename = _context->getInputFileName(_contextFileIdx);
- _bufStreamMgr = new BufferedStreamMgr(filename);
+ _filename = _context->getInputFileName(_contextFileIdx);
+ _bufStreamMgr = new BufferedStreamMgr(_filename);
if (!_bufStreamMgr->init()) {
- fprintf(stderr, "Error: unable to open file or unable to determine types for file %s.\n", filename.c_str());
+ cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
@@ -56,7 +56,7 @@ bool FileRecordMgr::open(){
_fileType = _bufStreamMgr->getTypeChecker().getFileType();
_recordType = _bufStreamMgr->getTypeChecker().getRecordType();
if (_fileType == FileRecordTypeChecker::UNKNOWN_FILE_TYPE || _recordType == FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
- fprintf(stderr, "Error: Unable to determine type for file %s.\n", filename.c_str());
+ cerr << "Error: Unable to determine type for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
@@ -64,11 +64,11 @@ bool FileRecordMgr::open(){
allocateFileReader();
_recordMgr = new RecordMgr(_recordType, _freeListBlockSize);
- _fileReader->setFileName(filename.c_str());
+ _fileReader->setFileName(_filename.c_str());
_fileReader->setInputStream(_bufStreamMgr);
_fileReader->setContext(_context);
if (!_fileReader->open()) {
- fprintf(stderr, "Error: Types determined but can't open file %s.\n", filename.c_str());
+ cerr << "Error: Types determined but can't open file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
@@ -125,6 +125,11 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
return NULL;
}
+ 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()) {
testInputSortOrder(record);
@@ -184,17 +189,16 @@ void FileRecordMgr::testInputSortOrder(Record *record)
void FileRecordMgr::sortError(const Record *record, bool genomeFileError)
{
if (genomeFileError) {
- fprintf(stderr, "Error: Sorted input specified, but the file %s has the following record with a different sort order than the genomeFile %s:\n",
- _context->getInputFileName(_contextFileIdx).c_str(), _context->getGenomeFile()->getGenomeFileName().c_str());
+ 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;
} else {
- fprintf(stderr, "Error: Sorted input specified, but the file %s has the following out of order record:\n", _context->getInputFileName(_contextFileIdx).c_str());
+ cerr << "Error: Sorted input specified, but the file " << _filename << " has the following out of order record" << endl;
}
- QuickString errBuf;
- record->print(errBuf);
- fprintf(stderr, "%s\n", errBuf.c_str());
+ cerr << *record << endl;
exit(1);
-
}
+
+
void FileRecordMgr::deleteRecord(const Record *record) {
_recordMgr->deleteRecord(record);
}
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
index 4c73d0faf25745c40e8ad705bcd96ea2cac92de3..cc176890616b58f019db498b7c37f99e1ce7f95c 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -141,6 +141,7 @@ public:
void setFullBamFlags(bool flag) { _useFullBamTags = flag; }
private:
+ QuickString _filename;
BufferedStreamMgr *_bufStreamMgr;
int _contextFileIdx;
diff --git a/src/utils/FileRecordTools/RecordOutputMgr.cpp b/src/utils/FileRecordTools/RecordOutputMgr.cpp
index 2ef905345ca1cdfd5558b3786225df2cb4853a08..984d6abadd2d33132d23f27885a869f9a3bc9cde 100644
--- a/src/utils/FileRecordTools/RecordOutputMgr.cpp
+++ b/src/utils/FileRecordTools/RecordOutputMgr.cpp
@@ -113,6 +113,7 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
_outBuf.append(_context->getHeader(_context->getQueryFileIdx()));
_context->setPrintHeader(false);
}
+ const_cast<Record *>(keyList.getKey())->undoZeroLength();
_currBlockList = blockList;
@@ -157,15 +158,67 @@ void RecordOutputMgr::printRecord(RecordKeyList &keyList, RecordKeyList *blockLi
void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record *hitRecord)
{
//get the max start and min end as strings.
- const QuickString &startStr = keyRecord->getStartPos() > hitRecord->getStartPos() ? keyRecord->getStartPosStr() : hitRecord->getStartPosStr();
- const QuickString &endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? keyRecord->getEndPosStr() : hitRecord->getEndPosStr();
+ const_cast<Record *>(hitRecord)->undoZeroLength();
- int maxStart = max(keyRecord->getStartPos(), hitRecord->getStartPos());
- int minEnd = min(keyRecord->getEndPos(), hitRecord->getEndPos());
+ const QuickString *startStr = NULL;
+ const QuickString *endStr = NULL;
+ int maxStart = 0;
+ int minEnd = 0;
+
+ int keyStart = keyRecord->getStartPos();
+ int keyEnd = keyRecord->getEndPos();
+ int hitStart = hitRecord->getStartPos();
+ int hitEnd = hitRecord->getEndPos();
+
+ if ( keyStart>= hitStart) {
+ //the key start is after the hit start, but we need to check and make sure the hit end is at least after the keyStart.
+ //The reason for this is that, in some rare cases, such as both the key and hit having been zero length intervals,
+ //the normal process for intersection that allows us to simply report the maxStart and minEnd do not necessarily apply.
+ if (hitEnd >= keyStart) {
+ //this is ok. We have a normal intersection where the key comes after the hit.
+
+ maxStart = keyStart;
+ startStr = &(keyRecord->getStartPosStr());
+
+ minEnd = min(keyEnd, hitEnd);
+ endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
+
+ } else {
+ //this is the weird case of not a "real" intersection. The keyStart is greater than the hitEnd. So just report the key as is.
+ maxStart = keyStart;
+ minEnd = keyEnd;
+ startStr = &(keyRecord->getStartPosStr());
+ endStr = &(keyRecord->getEndPosStr());
+ }
+
+ } else {
+ //all of the above, but backwards. keyStart is before hitStart.
+ if (keyEnd >= hitStart) {
+ //normal intersection, key first
+ maxStart = hitStart;
+ startStr = &(hitRecord->getStartPosStr());
+ minEnd = min(keyEnd, hitEnd);
+ endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? &(keyRecord->getEndPosStr()) : &(hitRecord->getEndPosStr());
+ } else {
+ //this is the weird case of not a "real" intersection. The hitStart is greater than the keyEnd. So just report the hit as is.
+ maxStart = hitStart;
+ minEnd = hitEnd;
+ startStr = &(hitRecord->getStartPosStr());
+ endStr = &(hitRecord->getEndPosStr());
+
+ }
+ }
+
+// const QuickString &startStr = keyRecord->getStartPos() > hitRecord->getStartPos() ? keyRecord->getStartPosStr() : hitRecord->getStartPosStr();
+// const QuickString &endStr = keyRecord->getEndPos() < hitRecord->getEndPos() ? keyRecord->getEndPosStr() : hitRecord->getEndPosStr();
+//
+// int maxStart = max(keyRecord->getStartPos(), hitRecord->getStartPos());
+// int minEnd = min(keyRecord->getEndPos(), hitRecord->getEndPos());
+//
if (!_context->getWriteA() && !_context->getWriteB() && !_context->getWriteOverlap() && !_context->getLeftJoin()) {
- printKey(keyRecord, startStr, endStr);
+ printKey(keyRecord, *startStr, *endStr);
newline();
}
else if ((_context->getWriteA() && _context->getWriteB()) || _context->getLeftJoin()) {
@@ -179,7 +232,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
newline();
}
else if (_context->getWriteB()) {
- printKey(keyRecord, startStr, endStr);
+ printKey(keyRecord, *startStr, *endStr);
tab();
hitRecord->print(_outBuf);
newline();
diff --git a/src/utils/FileRecordTools/Records/Bed4Interval.cpp b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
index eef359138455e71d6ac2f7cd233759fbfc8fab2a..13f5265e0c2310d6791b0e2c5dedbe0572b30795 100644
--- a/src/utils/FileRecordTools/Records/Bed4Interval.cpp
+++ b/src/utils/FileRecordTools/Records/Bed4Interval.cpp
@@ -23,6 +23,7 @@ bool Bed4Interval::initFromFile(SingleLineDelimTextFileReader *fileReader)
void Bed4Interval::print(QuickString &outBuf) const
{
Bed3Interval::print(outBuf);
+ outBuf.append('\t');
outBuf.append(_name);
}
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index 1f5351636aec2107915d9e89627d235bf570ef23..96e4eab004c41ca23193ab0384c43c1004d63c45 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -6,7 +6,8 @@ Record::Record()
: _chrId(-1),
_startPos(-1),
_endPos(-1),
- _strand(UNKNOWN)
+ _strand(UNKNOWN),
+ _zeroLength(false)
{
}
@@ -177,3 +178,37 @@ bool Record::sameChromIntersects(const Record *record,
return false;
}
+
+bool Record::coordsValid() {
+ if (_startPos < 0 || _endPos < 0 || _endPos < _startPos) {
+ return false;
+ }
+ adjustZeroLength();
+ return true;
+}
+
+void Record::adjustZeroLength()
+{
+ if (_startPos == _endPos) {
+ _zeroLength = true;
+ _startPos--;
+ _endPos++;
+ }
+}
+
+void Record::undoZeroLength()
+{
+ if (_zeroLength) {
+ _startPos++;
+ _endPos--;
+ _zeroLength = false;
+ }
+}
+
+ostream &operator << (ostream &out, const Record &record)
+{
+ QuickString errBuf;
+ record.print(errBuf);
+ out << errBuf;
+ return out;
+}
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 9dc1ae4e555fa7eb8e5f3a5a814296e09f351748..b2004231c14f41a4b316bfef155baaeeb5c96168 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -33,6 +33,8 @@ public:
virtual void print(QuickString &outBuf, int start, int end) const {}
virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end) const {}
virtual void printNull(QuickString &outBuf) const {}
+ friend ostream &operator << (ostream &out, const Record &record);
+
virtual const Record & operator=(const Record &);
virtual const QuickString &getChrName() const { return _chrName; }
@@ -54,13 +56,14 @@ public:
virtual const QuickString &getEndPosStr() const { return _endPosStr; }
virtual void setEndPosStr(const QuickString &str) { _endPosStr = str; }
+ virtual bool getZeroLength() const { return _zeroLength; }
+ virtual void setZeroLength(bool val) { _zeroLength = val; }
virtual strandType getStrand() const { return _strand; }
virtual void setStrand(strandType val) { _strand = val; }
virtual void setStrand(char val);
virtual char getStrandChar() const;
- //And we have a similar problem with name and score
virtual const QuickString &getName() const { return _name; }
virtual void setName(const QuickString &chr) { _name = chr; }
virtual void setName(const string &chr) { _name = chr; }
@@ -73,6 +76,18 @@ public:
virtual FileRecordTypeChecker::RECORD_TYPE getType() const { return FileRecordTypeChecker::UNKNOWN_RECORD_TYPE; }
+ virtual bool coordsValid(); //test that no coords negative, end not less than start, check zeroLength (see below).
+
+ //Some files can have insertions of the form 2,2. If found this should translate to cover the base before and after,
+ //thus meaning the startPos is decremented and the endPos is incremented. This method will find and handle that case.
+ //Don't adjust the startPosStr and endPosStr strings because they aren't used in
+ //calculation. They're only used in output, and it would be slower to change them
+ //and then change them back.
+ virtual void adjustZeroLength();
+ virtual void undoZeroLength(); //change it back just before output;
+ virtual bool isZeroLength() const { return _zeroLength; }
+
+
virtual bool operator < (const Record &other) const;
virtual bool operator > (const Record &other) const;
@@ -110,6 +125,7 @@ protected:
QuickString _name;
QuickString _score;
strandType _strand;
+ bool _zeroLength;
};