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Easier to print GenomeLoc compareTo() 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1597 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-09-12 19:10:35 +00:00
parent 3949b4ac72
commit 3ad97e4ab4
1 changed files with 18 additions and 10 deletions
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28
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -256,19 +256,27 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
} }
public int compareTo( GenomeLoc that ) { public int compareTo( GenomeLoc that ) {
if ( this == that ) return 0; int result = 0;
if ( this == that ) {
result = 0;
} else {
final int cmpContig = compareContigs(that);
final int cmpContig = compareContigs(that); if ( cmpContig != 0 ) {
result = cmpContig;
} else {
if ( this.getStart() < that.getStart() ) result = -1;
if ( this.getStart() > that.getStart() ) result = 1;
}
if ( cmpContig != 0 ) return cmpContig; // TODO: and error is being thrown because we are treating reads with the same start positions
if ( this.getStart() < that.getStart() ) return -1; // but different stop as out of order
if ( this.getStart() > that.getStart() ) return 1; //if ( this.getStop() < that.getStop() ) return -1;
//if ( this.getStop() > that.getStop() ) return 1;
}
// TODO: and error is being thrown because we are treating reads with the same start positions //System.out.printf("this vs. that = %s %s => %d%n", this, that, result);
// but different stop as out of order return result;
//if ( this.getStop() < that.getStop() ) return -1;
//if ( this.getStop() > that.getStop() ) return 1;
return 0;
} }
/** /**