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count X/N/etc. as mismatches for the NM attribute in the BAMs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1127 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-30 16:08:55 +00:00
parent d412c5dc2f
commit 08df4771c8
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
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@ -135,9 +135,10 @@ public class AlignmentUtils {
continue;
char refChr = refSeq.charAt(refIndex);
char readChr = readSeq.charAt(readIdx);
if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
BaseUtils.simpleBaseToBaseIndex(refChr) == -1 )
continue; // do not count Ns/Xs/etc ?
// Note: we need to count X/N's as mismatches because that's what SAM requires
//if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
// BaseUtils.simpleBaseToBaseIndex(refChr) == -1 )
// continue; // do not count Ns/Xs/etc ?
if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
mismatches++;
}