else if ( throughEndOfContigP() || getStart() == getStop() )
return String.format("%s:%d", getContig(), getStart());
else
return String.format("%s:%d-%d", getContig(), getStart(), getStop());
}
<BUG>public final boolean isUnmapped() { return this.contig == null; }
public final boolean throughEndOfContigP() { return this.stop == Integer.MAX_VALUE; }</BUG>
public final boolean atBeginningOfContigP() { return this.start == 1; }
public void setContig(String contig) {
<BUG>this.contig = contig;
}</BUG>
public void setStart(long start) {

else if ( throughEndOfContigP() || getStart() == getStop() )
return String.format("%s:%d", getContig(), getStart());
else
return String.format("%s:%d-%d", getContig(), getStart(), getStop());
}
public final boolean isUnmapped() { return this.contigIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX; }
public final boolean throughEndOfContigP() { return this.stop == Integer.MAX_VALUE; }
public final boolean atBeginningOfContigP() { return this.start == 1; }
public void setContig(String contig) {
this.contigIndex = contigInfo.getSequenceIndex(contig);
}
public void setStart(long start) {
