From 602239934347bcc3954ba8c38a39950907c746ae Mon Sep 17 00:00:00 2001
From: nkindlon <nek3d@virginia.edu>
Date: Tue, 24 Sep 2013 15:16:07 -0400
Subject: [PATCH] handling for unmapped Bam records
---
src/regressTest/RegressTest.cpp | 3 ++-
src/utils/FileRecordTools/FileRecordMgr.cpp | 18 +++++++++++++++---
.../FileRecordTools/Records/BamRecord.cpp | 1 +
src/utils/FileRecordTools/Records/BamRecord.h | 7 +++----
src/utils/FileRecordTools/Records/Record.cpp | 10 +++++++++-
src/utils/FileRecordTools/Records/Record.h | 6 ++++++
6 files changed, 36 insertions(+), 9 deletions(-)
diff --git a/src/regressTest/RegressTest.cpp b/src/regressTest/RegressTest.cpp
index 2612b8d4..4eaa8bcc 100644
--- a/src/regressTest/RegressTest.cpp
+++ b/src/regressTest/RegressTest.cpp
@@ -16,7 +16,8 @@ const string RegressTest::_randomCmd = "RANDOM";
const string RegressTest::_space = " ";
const string RegressTest::_redirect = " > ";
const string RegressTest::_devNull = " /dev/null ";
-const string RegressTest::_bedOpsCmd = "/home/nek3d/testWorkspace/bedops/bin/bedmap --echo --echo-map --bp-ovr 1 ";
+//const string RegressTest::_bedOpsCmd = "/home/nek3d/testWorkspace/bedops/bin/bedmap --echo --echo-map --bp-ovr 1 ";
+const string RegressTest::_bedOpsCmd = "/home/nek3d/testWorkspace/bedops/bin/bedops --intersect ";
RegressTest::RegressTest()
diff --git a/src/utils/FileRecordTools/FileRecordMgr.cpp b/src/utils/FileRecordTools/FileRecordMgr.cpp
index 0657e1eb..dfb5d4b5 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.cpp
+++ b/src/utils/FileRecordTools/FileRecordMgr.cpp
@@ -152,13 +152,25 @@ void FileRecordMgr::assignChromId(Record *record) {
void FileRecordMgr::testInputSortOrder(Record *record)
{
- //user specified that file must be sorted. Check that it is so.
+ // User specified that file must be sorted. Check that it is so.
// TBD: In future versions, we might not want/need all files to be sorted,
// even if the -sorted option is used, depending on number of input files
// and program being run. Should that occur, this block will need adjusting.
// NEK - 9/5/13
+
+ // 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()) {
+ return;
+ }
+
+
const QuickString &currChrom = record->getChrName();
+ int currStart = record->getStartPos();
+ if (record->isZeroLength()) {
+ currStart++;
+ }
if (currChrom != _prevChrom) {
if ( _foundChroms.find(currChrom) != _foundChroms.end()) {
//this is a different chrom than the last record had, but we've already seen this chrom.
@@ -179,10 +191,10 @@ void FileRecordMgr::testInputSortOrder(Record *record)
_prevStart = INT_MAX;
record->setChromId(_prevChromId);
}
- } else if (record->getStartPos() < _prevStart) { //same chrom as last record, but with lower startPos, so still out of order.
+ } else if (currStart < _prevStart) { //same chrom as last record, but with lower startPos, so still out of order.
sortError(record, false);
}
- _prevStart = record->getStartPos();
+ _prevStart = currStart;
}
diff --git a/src/utils/FileRecordTools/Records/BamRecord.cpp b/src/utils/FileRecordTools/Records/BamRecord.cpp
index ba7e1cc2..4b628613 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.cpp
+++ b/src/utils/FileRecordTools/Records/BamRecord.cpp
@@ -43,6 +43,7 @@ bool BamRecord::initFromFile(BamFileReader *bamFileReader)
setStrand(strandChar);
_bamAlignment = bamFileReader->getAlignment();
+ _isUnmapped = !_bamAlignment.IsMapped();
return true;
}
diff --git a/src/utils/FileRecordTools/Records/BamRecord.h b/src/utils/FileRecordTools/Records/BamRecord.h
index 574da454..bd275e79 100644
--- a/src/utils/FileRecordTools/Records/BamRecord.h
+++ b/src/utils/FileRecordTools/Records/BamRecord.h
@@ -39,14 +39,13 @@ public:
int getBamChromId() const { return _bamChromId; }
protected:
- virtual ~BamRecord();
- void printRemainingBamFields();
-
-
BamTools::BamAlignment _bamAlignment;
int _bamChromId; //different from chromId, because BAM file may be in different order
//than the genomeFile.
+ virtual ~BamRecord();
+ void printRemainingBamFields();
+
};
diff --git a/src/utils/FileRecordTools/Records/Record.cpp b/src/utils/FileRecordTools/Records/Record.cpp
index 96e4eab0..f4203153 100644
--- a/src/utils/FileRecordTools/Records/Record.cpp
+++ b/src/utils/FileRecordTools/Records/Record.cpp
@@ -7,7 +7,8 @@ Record::Record()
_startPos(-1),
_endPos(-1),
_strand(UNKNOWN),
- _zeroLength(false)
+ _zeroLength(false),
+ _isUnmapped(false)
{
}
@@ -35,6 +36,9 @@ void Record::clear() {
_strand = UNKNOWN;
_startPosStr.clear();
_endPosStr.clear();
+ _zeroLength = false;
+ _isUnmapped = false;
+
}
void Record::setStrand(char val)
@@ -130,6 +134,10 @@ bool Record::intersects(const Record *record,
bool Record::sameChromIntersects(const Record *record,
bool wantSameStrand, bool wantDiffStrand, float overlapFraction, bool reciprocal) const
{
+ // Special: For BAM records that are unmapped, intersect should automatically return false
+ if (_isUnmapped || record->_isUnmapped) {
+ return false;
+ }
//If user requested hits only on same strand, or only on different strands,
//rule out different strandedness first.
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index b2004231..47cf3b34 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -87,6 +87,11 @@ public:
virtual void undoZeroLength(); //change it back just before output;
virtual bool isZeroLength() const { return _zeroLength; }
+ // "Unmapped" only applies to BamRecord, but for design reasons, it has to be here,
+ // because we want to short circuit the intersects method if either record is an unmapped
+ // Bam record.
+ bool isUnmapped() const { return _isUnmapped; }
+
virtual bool operator < (const Record &other) const;
virtual bool operator > (const Record &other) const;
@@ -126,6 +131,7 @@ protected:
QuickString _score;
strandType _strand;
bool _zeroLength;
+ bool _isUnmapped;
};
--
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