zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
View File

@ -135,9 +135,10 @@ public class AlignmentUtils {
continue; continue;
char refChr = refSeq.charAt(refIndex); char refChr = refSeq.charAt(refIndex);
char readChr = readSeq.charAt(readIdx); char readChr = readSeq.charAt(readIdx);
if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 || // Note: we need to count X/N's as mismatches because that's what SAM requires
BaseUtils.simpleBaseToBaseIndex(refChr) == -1 ) //if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 ||
continue; // do not count Ns/Xs/etc ? // BaseUtils.simpleBaseToBaseIndex(refChr) == -1 )
// continue; // do not count Ns/Xs/etc ?
if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) ) if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
mismatches++; mismatches++;
} }