public GenomeLoc( final String contig, final long pos ) {
this( contig, pos, pos );
}</BUG>
public GenomeLoc( final GenomeLoc toCopy ) {
<BUG>this( new String(toCopy.getContig()), toCopy.getStart(), toCopy.getStop() );
</BUG>
}
public static GenomeLoc genomicLocationOf(final SAMRecord read) {
<BUG>String contig = read.getReferenceName();
if (read.getReadUnmappedFlag())
contig = null;
return new GenomeLoc(contig, read.getAlignmentStart(), read.getAlignmentEnd());
</BUG>
}

public GenomeLoc( final String contig, final long pos ) {
this(contig, pos, pos );
}
public GenomeLoc( final int contig, final long pos ) {
this(contig, pos, pos );
}
public GenomeLoc( final GenomeLoc toCopy ) {
this( toCopy.contigIndex, toCopy.getStart(), toCopy.getStop() );
}
public static GenomeLoc genomicLocationOf(final SAMRecord read) {
return new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd());
}
