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refactored to provide a sum of mismatch quality scores capability as well (used by Cancer) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2911 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2010-03-02 16:40:03 +00:00
parent 91b3f9745e
commit 7578678f99
1 changed files with 16 additions and 5 deletions
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21
java/src/org/broadinstitute/sting/utils/AlignmentUtils.java
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@ -194,13 +194,25 @@ public class AlignmentUtils {
* @return the number of mismatches
*/
public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, boolean ignoreTargetSite) {
return mismatchesInRefWindow(p, ref, ignoreTargetSite, false);
}
int mismatches = 0;
/** Returns the number of mismatches in the pileup element within the given reference context.
*
* @param p the pileup element
* @param ref the reference context
* @param ignoreTargetSite if true, ignore mismatches at the target locus (i.e. the center of the window)
* @param qualitySumInsteadOfMismatchCount if true, return the quality score sum of the mismatches rather than the count
* @return the number of mismatches
*/
public static int mismatchesInRefWindow(PileupElement p, ReferenceContext ref, boolean ignoreTargetSite, boolean qualitySumInsteadOfMismatchCount) {
int sum = 0;
int windowStart = (int)ref.getWindow().getStart();
int windowStop = (int)ref.getWindow().getStop();
char[] refBases = ref.getBases();
byte[] readBases = p.getRead().getReadBases();
byte[] readQualities = p.getRead().getBaseQualities();
Cigar c = p.getRead().getCigar();
int readIndex = 0;
@ -228,8 +240,8 @@ public class AlignmentUtils {
continue;
char readChr = (char)readBases[readIndex];
if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
mismatches++;
if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) )
sum += (qualitySumInsteadOfMismatchCount) ? readQualities[readIndex] : 1;
}
break;
case I:
@ -246,10 +258,9 @@ public class AlignmentUtils {
// fail silently
return 0;
}
}
return mismatches;
return sum;
}
/** Returns number of alignment blocks (continuous stretches of aligned bases) in the specified alignment.