if ( match1.matches() ) {
contig = match1.group(1);
}
else if ( match2.matches() ) {
contig = match2.group(1);
<BUG>start = parsePosition(match2.group(2));
}</BUG>
else if ( match3.matches() ) {
contig = match3.group(1);
start = parsePosition(match3.group(2));

if ( match1.matches() ) {
contig = match1.group(1);
}
else if ( match2.matches() ) {
contig = match2.group(1);
start = parsePosition(match2.group(2));
stop = start;
}
else if ( match3.matches() ) {
contig = match3.group(1);
start = parsePosition(match3.group(2));
