Pair-end reads: if only one mate aligns, force align the other mate to the same position
Hamdist skip match interval
Cigar: should not exceed the begin/end of chromo
Add command line in the sam header (@CL)
Update the get_tid func based on the yeast genome
Pair-end reads: if only one mate aligns, force align the other mate to the same position Hamdist skip match interval Cigar: should not exceed the begin/end of chromo Add command line in the sam header (@CL) Update the get_tid func based on the yeast genome