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more comparisons 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1059 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-19 16:46:05 +00:00
parent 58b132ee10
commit aef519b427
1 changed files with 20 additions and 3 deletions
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23
java/src/org/broadinstitute/sting/utils/ComparableSAMRecord.java
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@ -5,9 +5,11 @@ import net.sf.samtools.SAMRecord;
public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> { public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
private SAMRecord record; private SAMRecord record;
private GenomeLoc loc;
public ComparableSAMRecord(SAMRecord record) { public ComparableSAMRecord(SAMRecord record) {
this.record = record; this.record = record;
this.loc = new GenomeLoc(record);
} }
public SAMRecord getRecord() { public SAMRecord getRecord() {
@ -16,13 +18,28 @@ public class ComparableSAMRecord implements Comparable<ComparableSAMRecord> {
public int compareTo(ComparableSAMRecord o) { public int compareTo(ComparableSAMRecord o) {
// first sort by start position // first sort by start position
GenomeLoc myLoc = new GenomeLoc(record); int comparison = loc.compareTo(o.loc);
GenomeLoc hisLoc = new GenomeLoc(o.getRecord());
int comparison = myLoc.compareTo(hisLoc);
// if the reads have the same start position, we must give a non-zero comparison // if the reads have the same start position, we must give a non-zero comparison
// (because java Sets often require "consistency with equals") // (because java Sets often require "consistency with equals")
if ( comparison == 0 ) if ( comparison == 0 )
comparison = record.getReadName().compareTo(o.getRecord().getReadName()); comparison = record.getReadName().compareTo(o.getRecord().getReadName());
// if the read names are the same, use the first of the pair if appropriate
if ( comparison == 0 )
comparison = ( record.getFirstOfPairFlag() ? -1 : 1);
return comparison; return comparison;
} }
public boolean equals(Object obj) {
if ( !(obj instanceof ComparableSAMRecord) )
return false;
if ( this == obj )
return true;
ComparableSAMRecord csr = (ComparableSAMRecord)obj;
if ( loc.compareTo(csr.loc) != 0 )
return false;
if ( !record.getReadName().equals(csr.getRecord().getReadName()) )
return false;
return ( record.getFirstOfPairFlag() == csr.record.getFirstOfPairFlag() );
}
} }