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/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 e9861b9e93ccc28bdf7347bec90af23165284a02..8bea945ed8b1bdbecfaec9e8e20d82bf6e26f295 100644
--- a/src/utils/FileRecordTools/FileReaders/BamFileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
@@ -58,7 +58,6 @@ protected:
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/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 8b3c2cadcf79609ace299dec0b3d3b5d999d63bd..38fc056b483236611748943ebcce4a7228f0a95f 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -30,19 +30,15 @@ FileRecordMgr::FileRecordMgr(const QuickString &filename, bool isSorted)
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(){
@@ -78,10 +74,9 @@ bool FileRecordMgr::open(){
}
void FileRecordMgr::close(){
- if (_bufStreamMgr != NULL) {
- delete _bufStreamMgr;
- _bufStreamMgr = NULL;
- }
+ delete _bufStreamMgr;
+ _bufStreamMgr = NULL;
+
if (_fileReader != NULL) {
_fileReader->close();
delete _fileReader;
@@ -91,7 +86,6 @@ void FileRecordMgr::close(){
bool FileRecordMgr::eof(){
return _fileReader->eof();
-// return _storedRecords.empty() && _fileReader->eof() ? true: false;
}
Record *FileRecordMgr::allocateAndGetNextRecord()
@@ -109,8 +103,9 @@ 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->coordsValid()) {
diff --git a/src/utils/NewChromsweep/NewChromsweep.cpp b/src/utils/NewChromsweep/NewChromsweep.cpp
index 14e9a908f0dbfbc425718956af0afa50964ebd61..5e6045be625799cca515ac056e9a17b33f1908a6 100644
--- a/src/utils/NewChromsweep/NewChromsweep.cpp
+++ b/src/utils/NewChromsweep/NewChromsweep.cpp
@@ -68,12 +68,12 @@ NewChromSweep::~NewChromSweep(void) {
if (!_wasInitialized) {
return;
}
- if (_currQueryRec != NULL) {
- _queryFRM->deleteRecord(_currQueryRec);
- }
- if (_currDatabaseRec != NULL) {
- _databaseFRM->deleteRecord(_currDatabaseRec);
- }
+ _queryFRM->deleteRecord(_currQueryRec);
+ _currQueryRec = NULL;
+
+ _databaseFRM->deleteRecord(_currDatabaseRec);
+ _currDatabaseRec = NULL;
+
_queryFRM->close();
_databaseFRM->close();
}