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Fixed interval navigation bug. 

If a read was hard clipped away from the current interval, all subsequent reads within that interval (not hardclipped) would be filtered out. Fixed.
This commit is contained in:
Mauricio Carneiro 2011-09-26 08:13:44 -04:00
parent 9afccd11b1
commit b76dbc72f0
1 changed files with 18 additions and 10 deletions
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28
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -157,7 +157,7 @@ public class ReadUtils {
* |----------------| (interval)
* <--------> (read)
*/
public enum ReadAndIntervalOverlap {NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT, NO_OVERLAP_RIGHT, OVERLAP_LEFT, OVERLAP_RIGHT, OVERLAP_LEFT_AND_RIGHT, OVERLAP_CONTAINED}
public enum ReadAndIntervalOverlap {NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT, NO_OVERLAP_RIGHT, NO_OVERLAP_HARDCLIPPED_LEFT, NO_OVERLAP_HARDCLIPPED_RIGHT, OVERLAP_LEFT, OVERLAP_RIGHT, OVERLAP_LEFT_AND_RIGHT, OVERLAP_CONTAINED}
/**
* God, there's a huge information asymmetry in SAM format:
@ -640,27 +640,35 @@ public class ReadUtils {
*/
public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) {
int start = getRefCoordSoftUnclippedStart(read);
int stop = getRefCoordSoftUnclippedEnd(read);
int sStart = getRefCoordSoftUnclippedStart(read);
int sStop = getRefCoordSoftUnclippedEnd(read);
int uStart = read.getUnclippedStart();
int uStop = read.getUnclippedEnd();
if ( !read.getReferenceName().equals(interval.getContig()) )
return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG;
else if ( stop < interval.getStart() )
else if ( uStop < interval.getStart() )
return ReadAndIntervalOverlap.NO_OVERLAP_LEFT;
else if ( start > interval.getStop() )
else if ( uStart > interval.getStop() )
return ReadAndIntervalOverlap.NO_OVERLAP_RIGHT;
else if ( (start >= interval.getStart()) &&
(stop <= interval.getStop()) )
else if ( sStop < interval.getStart() )
return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_LEFT;
else if ( sStart > interval.getStop() )
return ReadAndIntervalOverlap.NO_OVERLAP_HARDCLIPPED_RIGHT;
else if ( (sStart >= interval.getStart()) &&
(sStop <= interval.getStop()) )
return ReadAndIntervalOverlap.OVERLAP_CONTAINED;
else if ( (start < interval.getStart()) &&
(stop > interval.getStop()) )
else if ( (sStart < interval.getStart()) &&
(sStop > interval.getStop()) )
return ReadAndIntervalOverlap.OVERLAP_LEFT_AND_RIGHT;
else if ( (start < interval.getStart()) )
else if ( (sStart < interval.getStart()) )
return ReadAndIntervalOverlap.OVERLAP_LEFT;
else