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added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1130 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-30 17:40:37 +00:00
parent 9fca79ed62
commit 177d6d00b8
1 changed files with 12 additions and 2 deletions
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14
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -146,10 +146,22 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
public final boolean throughEndOfContigP() { return this.stop == Integer.MAX_VALUE; }
public final boolean atBeginningOfContigP() { return this.start == 1; }
/** Sets contig name. UNSAFE since it 1) does NOT update contig index; 2) does not validate the name
*
* @param contig
*/
public void setContig(String contig) {
this.contigName = contig;
}
/** Sets contig index. UNSAFE since it 1) does NOT update contig name; 2) does not validate the index
*
* @param contig
*/
public void setContigIndex(int contig) {
this.contigIndex = contig;
}
public void setStart(long start) {
this.start = start;
}
@ -296,6 +308,4 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
}