public final boolean containsP(GenomeLoc that) {
if ( ! onSameContig(that) ) return false;
return getStart() <= that.getStart() && getStop() >= that.getStop();
}
public final boolean onSameContig(GenomeLoc that) {
<BUG>return this.contig.equals(that.contig);
</BUG>
}
public final int minus( final GenomeLoc that ) {
<BUG>if ( this.getContig().equals(that.getContig()) )
return (int) (this.getStart() - that.getStart());</BUG>
else

public final boolean containsP(GenomeLoc that) {
if ( ! onSameContig(that) ) return false;
return getStart() <= that.getStart() && getStop() >= that.getStop();
}
public final boolean onSameContig(GenomeLoc that) {
return (this.contigIndex == that.contigIndex);
}
public final int minus( final GenomeLoc that ) {
if ( this.contigIndex == that.contigIndex )
return (int) (this.getStart() - that.getStart());
else
