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Fix for the HaplotypeScore optimization in AlignmentUtils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5310 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-02-24 20:40:18 +00:00
parent 15dfac6bf7
commit 1129f1535d
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -70,7 +70,7 @@ public class AlignmentUtils {
* on the read of length <code>nReadBases</code> starting at (0-based) position <code>readIndex</code>.
* @param r Aligned read to count mismatches for
* @param refSeq Chunk of reference sequence that subsumes the alignment
* @param refIndex Zero-based position on <code>refSeq</code> where the alighnment for the whole read starts
* @param refIndex Zero-based position on <code>refSeq</code> where the alignment for the whole read starts
* @param readIndex Zero-based position on the read, the mismatches will be counted only from this position on
* @param nReadBases Length of continuous stretch on the read, along which mismatches will be counted
* @return
@ -491,7 +491,7 @@ public class AlignmentUtils {
if(!atDeletion) {
alignmentPos += elementLength;
} else {
if( pos + elementLength >= pileupOffset ) {
if( pos + elementLength - 1 >= pileupOffset ) {
return alignmentPos + (pileupOffset - pos);
} else {
pos += elementLength;
@ -500,7 +500,7 @@ public class AlignmentUtils {
}
break;
case M:
if( pos + elementLength >= pileupOffset ) {
if( pos + elementLength - 1 >= pileupOffset ) {
return alignmentPos + (pileupOffset - pos);
} else {
pos += elementLength;
@ -602,7 +602,7 @@ public class AlignmentUtils {
if ( r.getReadUnmappedFlag() ) return true;
// our life would be so much easier if all sam files followed the specs. In reality,
// sam files (including those generated by maq or bwa) miss headers alltogether. When
// sam files (including those generated by maq or bwa) miss headers altogether. When
// reading such a SAM file, reference name is set, but since there is no sequence dictionary,
// null is always returned for referenceIndex. Let's be paranoid here, and make sure that
// we do not call the read "unmapped" when it has only reference name set with ref. index missing
@ -624,7 +624,7 @@ public class AlignmentUtils {
if ( r.getMateUnmappedFlag() ) return true;
// our life would be so much easier if all sam files followed the specs. In reality,
// sam files (including those generated by maq or bwa) miss headers alltogether. When
// sam files (including those generated by maq or bwa) miss headers altogether. When
// reading such a SAM file, reference name is set, but since there is no sequence dictionary,
// null is always returned for referenceIndex. Let's be paranoid here, and make sure that
// we do not call the read "unmapped" when it has only reference name set with ref. index missing