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bug fixed when a read with alignment end exactly at the window boundary and with last cigar element being an indel would cause index-out-of-bounds exception 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@992 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-11 21:03:15 +00:00
parent a12009e9e7
commit d5cd883b99
1 changed files with 30 additions and 5 deletions
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35
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -10,6 +10,7 @@ import java.util.Set;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
@ -27,6 +28,9 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="somatic", shortName="somatic",
doc="Perform somatic calls; two input alignment files must be specified", required=false)
public boolean call_somatic = false;
@Argument(fullName="verbose", shortName="verbose",
doc="Tell us what you are calling now (printed to stdout)", required=false)
public boolean verbose = false;
private static int WINDOW_SIZE = 200;
private RunningCoverage coverage;
@ -141,12 +145,25 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
throw new StingException("Read "+read.getReadName()+": out of order on the contig");
}
// a little trick here: we want to make sure that current read completely fits into the current
// window so that we can accumulate the coverage/indel counts over the whole length of the read.
// The ::getAlignmentEnd() method returns the last position on the reference where bases from the
// read actually match (M or D cigar elements). After our cleaning procedure, we can have reads that end
// with I element, which is not gonna be counted into alignment length on the reference. On the other hand,
// in this program we assign insertions, internally, to the first base *after* the insertion position.
// Hence, we have to make sure that that extra base is already in the window or we will get IndexOutOfBounds.
if ( read.getAlignmentEnd() > coverage.getStop()) {
long alignmentEnd = read.getAlignmentEnd();
Cigar c = read.getCigar();
if ( c.getCigarElement(c.numCigarElements()-1).getOperator() == CigarOperator.I) alignmentEnd++;
if ( alignmentEnd > coverage.getStop()) {
// we don't emit anything until we reach a read that does not fit into the current window.
// At that point we shift the window to the start of that read and emit everything prior to
// that position (reads are sorted, so we are not gonna see any more coverage at those lower positions)
// that position (reads are sorted, so we are not gonna see any more coverage at those lower positions).
// Clearly, we assume here that window is large enough to accomodate any single read, so simply shifting
// the window to the read's start will ensure that the read fits...
if ( call_somatic ) emit_somatic( read.getAlignmentStart() );
else emit( read.getAlignmentStart() );
@ -287,7 +304,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
} else {
message += "\tGERMLINE";
}
logger.info(message);
if ( verbose ) System.out.println(message);
}
// for ( IndelVariant var : variants ) {
// System.out.print("\t"+var.getType()+"\t"+var.getBases()+"\t"+var.getCount());
@ -467,7 +484,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
// will increment position on the read below, there's no 'break' statement yet...
case H:
case S:
// here we also skip hard and soft-clipped bases on th eread; according to SAM format specification,
// here we also skip hard and soft-clipped bases on the read; according to SAM format specification,
// alignment start position on the reference points to where the actually aligned
// (not clipped) bases go, so we do not need to increment reference position here
posOnRead += ce.getLength();
@ -492,7 +509,15 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( i == 0 ) logger.warn("Indel at the start of the read "+r.getReadName());
if ( i == nCigarElems - 1) logger.warn("Indel at the end of the read "+r.getReadName());
updateCount(indelPosition, type, bases);
try {
updateCount(indelPosition, type, bases);
} catch (IndexOutOfBoundsException e) {
System.out.println("Read "+r.getReadName()+": out of coverage window bounds.Probably window is too small.\n"+
"Read length="+r.getReadLength()+"; cigar="+r.getCigarString()+"; start="+
r.getAlignmentStart()+"; end="+r.getAlignmentEnd()+"; window start="+getStart()+
"; window end="+getStop());
throw e;
}
}