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moved another variant of numMismatches to AlignmentUtils 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@921 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-06 18:05:29 +00:00
parent e6aa058ec4
commit 7018dd1469
1 changed files with 10 additions and 29 deletions
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39
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
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@ -58,6 +58,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
try { try {
indelOutput = new FileWriter(new File(OUT_INDELS)); indelOutput = new FileWriter(new File(OUT_INDELS));
} catch (Exception e) { } catch (Exception e) {
logger.warn("Failed to create output file "+ OUT_INDELS+". Indel output will be suppressed");
err.println(e.getMessage()); err.println(e.getMessage());
indelOutput = null; indelOutput = null;
} }
@ -66,6 +67,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
try { try {
statsOutput = new FileWriter(new File(OUT_STATS)); statsOutput = new FileWriter(new File(OUT_STATS));
} catch (Exception e) { } catch (Exception e) {
logger.warn("Failed to create output file "+ OUT_STATS+". Cleaning stats output will be suppressed");
err.println(e.getMessage()); err.println(e.getMessage());
statsOutput = null; statsOutput = null;
} }
@ -83,7 +85,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
try { try {
writer.addAlignment(read); writer.addAlignment(read);
} catch (Exception e ) { } catch (Exception e ) {
logger.error("Failed to write read "+read.getReadName()+" "+read.getReferenceName() +":"+read.getAlignmentStart()); logger.error("Failed to write read "+read.getReadName()+" aligned at "+read.getReferenceName() +":"+read.getAlignmentStart());
e.printStackTrace(out); e.printStackTrace(out);
throw new StingException(e.getMessage()); throw new StingException(e.getMessage());
} }
@ -129,41 +131,20 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( OUT_INDELS != null ) { if ( OUT_INDELS != null ) {
try { try {
indelOutput.close(); indelOutput.close();
} catch (Exception e) {} } catch (Exception e) {
logger.error("Failed to close "+OUT_INDELS+" gracefully. Data may be corrupt.");
}
} }
if ( OUT_STATS != null ) { if ( OUT_STATS != null ) {
try { try {
statsOutput.close(); statsOutput.close();
} catch (Exception e) {} } catch (Exception e) {
} logger.error("Failed to close "+OUT_STATS+" gracefully. Data may be corrupt.");
}
private static int numMismatches(SAMRecord r, String refSeq, int refIndex) {
int readIdx = 0;
int mismatches = 0;
String readSeq = r.getReadString();
Cigar c = r.getCigar();
for (int i = 0 ; i < c.numCigarElements() ; i++) {
CigarElement ce = c.getCigarElement(i);
switch ( ce.getOperator() ) {
case M:
for (int j = 0 ; j < ce.getLength() ; j++, refIndex++, readIdx++ ) {
if ( Character.toUpperCase(readSeq.charAt(readIdx)) != Character.toUpperCase(refSeq.charAt(refIndex)) )
mismatches++;
}
break;
case I:
readIdx += ce.getLength();
break;
case D:
refIndex += ce.getLength();
break;
} }
} }
return mismatches;
} }
private static int mismatchQualitySum(AlignedRead aRead, String refSeq, int refIndex) { private static int mismatchQualitySum(AlignedRead aRead, String refSeq, int refIndex) {
String readSeq = aRead.getReadString(); String readSeq = aRead.getReadString();
String quals = aRead.getBaseQualityString(); String quals = aRead.getBaseQualityString();
@ -370,7 +351,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
AlignedRead aRead = altReads.get(indexPair.first); AlignedRead aRead = altReads.get(indexPair.first);
aRead.finalizeUpdate(); aRead.finalizeUpdate();
aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)improvement, 255)); aRead.getRead().setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + (int)improvement, 255));
aRead.getRead().setAttribute("NM", numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex)); aRead.getRead().setAttribute("NM", AlignmentUtils.numMismatches(aRead.getRead(), reference, aRead.getRead().getAlignmentStart()-(int)leftmostIndex));
} }
} }
} else if ( statsOutput != null ) { } else if ( statsOutput != null ) {