Exiting from the software immediately after visiting unmapped reads

[mahdiheydari]

The software is working very good, except the case when an unmapped read is in the middle of SAM file. Then it exits the software with this message

shift_cigar failed. Exiting.

Is it possible you scape these reads or other reads which for any reason you can't align instead of exiting the software? Just to keep the order of reads as the input file, I would suggest for these unmapped reads you put a flag in the output or show the aligned read with all N, or another character to make difference between soft clipping and unmapped reads.

[y9c]

samtools view -F 4 test.sam | sam2pairwise

might solve the issue