From 6817f60adad4f4a924089d044f0f85dfab088f96 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 11 Oct 2011 08:28:28 -0400
Subject: [PATCH] getBamBlocks no longer splits on D CIGAR ops when not wanted.
---
src/utils/BamTools-Ancillary/BamAncillary.cpp | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/src/utils/BamTools-Ancillary/BamAncillary.cpp b/src/utils/BamTools-Ancillary/BamAncillary.cpp
index 92b02558..54e89f1a 100644
--- a/src/utils/BamTools-Ancillary/BamAncillary.cpp
+++ b/src/utils/BamTools-Ancillary/BamAncillary.cpp
@@ -27,15 +27,21 @@ namespace BamTools {
string name = bam.Name;
string strand = "+";
string score = ToString(bam.MapQuality);
+ char prevOp = '\0';
if (bam.IsReverseStrand()) strand = "-";
+ bool blocksFound = false;
vector<CigarOp>::const_iterator cigItr = bam.CigarData.begin();
vector<CigarOp>::const_iterator cigEnd = bam.CigarData.end();
for ( ; cigItr != cigEnd; ++cigItr ) {
if (cigItr->Type == 'M') {
currPosition += cigItr->Length;
- blocks.push_back( BED(chrom, blockStart, currPosition, name, score, strand) );
- blockStart = currPosition;
+ // we only want to create a new block if the current M op
+ // was preceded by an N op or a D op (and we are breaking on D ops)
+ if ((prevOp == 'D' && breakOnDeletionOps == true) || (prevOp == 'N')) {
+ blocks.push_back( BED(chrom, blockStart, currPosition, name, score, strand) );
+ blockStart = currPosition;
+ }
}
else if (cigItr->Type == 'D') {
if (breakOnDeletionOps == false)
@@ -47,7 +53,8 @@ namespace BamTools {
}
else if (cigItr->Type == 'N') {
currPosition += cigItr->Length;
- blockStart = currPosition; }
+ blockStart = currPosition;
+ }
else if (cigItr->Type == 'S' || cigItr->Type == 'H' || cigItr->Type == 'P' || cigItr->Type == 'I') {
// do nothing
}
@@ -56,6 +63,11 @@ namespace BamTools {
<< ") for: " << bam.Name << endl;
exit(1);
}
+ prevOp = cigItr->Type;
+ }
+ // if there were no splits, we just create a block representing the contiguous alignment.
+ if (blocksFound == false) {
+ blocks.push_back( BED(chrom, bam.Position, currPosition, name, score, strand) );
}
}
}
--
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