From 79daf360c40700ee26045f753ec0ceedaf044643 Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Sat, 28 Sep 2013 21:02:30 -0400
Subject: [PATCH] Fixed unmapped mate bug
---
src/utils/BinTree/BinTree.cpp | 2 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 12 +++++++-----
src/utils/FileRecordTools/Records/BamRecord.cpp | 1 +
src/utils/FileRecordTools/Records/Record.cpp | 5 +++--
src/utils/FileRecordTools/Records/Record.h | 2 ++
5 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/src/utils/BinTree/BinTree.cpp b/src/utils/BinTree/BinTree.cpp
index 36e5b36e..12da7a1e 100644
--- a/src/utils/BinTree/BinTree.cpp
+++ b/src/utils/BinTree/BinTree.cpp
@@ -111,6 +111,7 @@ void BinTree::getHits(Record *record, RecordKeyList &hitSet)
if (_showBinMetrics) {
return; //don't care about query entries just yet.
}
+
const QuickString &chr = record->getChrName();
mainMapType::iterator mainIter = _mainMap.find(chr);
if (mainIter == _mainMap.end()) {
@@ -173,7 +174,6 @@ bool BinTree::addRecordToTree(const Record *record)
uint32_t startPos = (uint32_t)(record->getStartPos());
uint32_t endPos = (uint32_t)(record->getEndPos());
-
//is this chr currently in the main map?
allBinsType bins = NULL;
mainMapType::iterator mainIter = _mainMap.find(chr);
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index 2931286e..08998aaa 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -124,7 +124,12 @@ Record *FileRecordMgr::allocateAndGetNextRecord()
_recordMgr->deleteRecord(record);
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 (record->isUnmapped() && record->isMateUnmapped()) {
+ _recordMgr->deleteRecord(record);
+ return NULL;
+ }
if (!record->coordsValid()) {
cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
exit(1);
@@ -160,7 +165,7 @@ void FileRecordMgr::testInputSortOrder(Record *record)
// Special: For BAM records that aren't mapped, we actually don't want
// to test the sort order. Another ugly hack sponsored by the letters B, A, and M.
- if (record->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE && (static_cast<const BamRecord *>(record))->isUnmapped()) {
+ if (record->isUnmapped()) {
return;
}
@@ -269,9 +274,6 @@ bool FileRecordMgr::allocateAndGetNextMergedRecord(RecordKeyList & recList, WANT
startRecord = NULL;
}
}
- if (startRecord->getStartPos() == 107071272) {
- printf("Break point.\n");
- }
// OK!! We have a start record!
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index 4b628613..39096456 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -44,6 +44,7 @@ bool BamRecord::initFromFile(BamFileReader *bamFileReader)
_bamAlignment = bamFileReader->getAlignment();
_isUnmapped = !_bamAlignment.IsMapped();
+ _isMateUnmapped = !_bamAlignment.IsMateMapped();
return true;
}
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index f4203153..e5bc1e6f 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -8,7 +8,8 @@ Record::Record()
_endPos(-1),
_strand(UNKNOWN),
_zeroLength(false),
- _isUnmapped(false)
+ _isUnmapped(false),
+ _isMateUnmapped(false)
{
}
@@ -38,7 +39,7 @@ void Record::clear() {
_endPosStr.clear();
_zeroLength = false;
_isUnmapped = false;
-
+ _isMateUnmapped = false;
}
void Record::setStrand(char val)
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 47cf3b34..9c5c3ff1 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -91,6 +91,7 @@ public:
// because we want to short circuit the intersects method if either record is an unmapped
// Bam record.
bool isUnmapped() const { return _isUnmapped; }
+ bool isMateUnmapped() const { return _isMateUnmapped; }
virtual bool operator < (const Record &other) const;
@@ -132,6 +133,7 @@ protected:
strandType _strand;
bool _zeroLength;
bool _isUnmapped;
+ bool _isMateUnmapped;
};
--
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