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Uses the cleaner new GenomeLoc(read) syntax 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-14 00:55:43 +00:00
parent 1cee7948ab
commit 8b2c2e677b
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
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@ -113,7 +113,8 @@ public class LocusIteratorByHanger extends LocusIterator {
} }
protected void hangRead(final SAMRecord read) { protected void hangRead(final SAMRecord read) {
GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart()); //GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart());
GenomeLoc readLoc = new GenomeLoc(read);
//System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart()); //System.out.printf("Adding read %s at %d%n", read.getReadName(), read.getAlignmentStart());
/* /*
@ -155,7 +156,7 @@ public class LocusIteratorByHanger extends LocusIterator {
return true; return true;
else { else {
final SAMRecord read = it.peek(); final SAMRecord read = it.peek();
GenomeLoc readLoc = GenomeLoc.genomicLocationOf(read); GenomeLoc readLoc = new GenomeLoc(read);
final boolean coveredP = currentPositionIsFullyCovered(readLoc); final boolean coveredP = currentPositionIsFullyCovered(readLoc);
//System.out.printf("CoverP = %s => %b%n", readLoc, coveredP); //System.out.printf("CoverP = %s => %b%n", readLoc, coveredP);
return coveredP; return coveredP;
@ -177,7 +178,7 @@ public class LocusIteratorByHanger extends LocusIterator {
SAMRecord read = it.next(); SAMRecord read = it.next();
justCleared = false; justCleared = false;
GenomeLoc readLoc = GenomeLoc.genomicLocationOf(read); GenomeLoc readLoc = new GenomeLoc(read);
if ( DEBUG ) { if ( DEBUG ) {
logger.debug(String.format(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n", logger.debug(String.format(" Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d%n",
readHanger.size(), incrementSize, readHanger.size(), incrementSize,