mjafin/splitnreads

splitNreads

splitnreads's Issues

[Bug] Splitting reads into three or more parts

Dear @mjafin,
thank you for the tool, which is very helpful. However, I got stuck while splitting reads containing two or more N cigars:

18M2443N77M2449N5M TAGGGGCTCCCGCTGCAGCTCTTTCACTTCCACAAGACCAGAAAGAGTCAGGGCTGAACACAGCTTAGATGCTGTCTTCACTTTGCTATTGTTATCTACA
--- becomes: ---
18M4974H           TAGGGGCTCCCGCTGCAG
2461H77M2454H                        CTCTTTCACTTCCACAAGACCAGAAAGAGTCAGGGCTGAACACAGCTTAGATGCTGTCTTCACTTTGCTATTGTTATCTACA
4987H5M                                                                                                           CTACA

Obviously, the second sequence is too long which also holds for the quality string. This happens as a result of your code in lines 80 and 82 extracting the sequence/quality substring. In both, change start_pos:start_pos+offset to start_pos:offset because offset already contains the absolute end position.

This is not a problem for splits of reads containing one N but clearly for reads containing more.

Thank you for your work,
Manuel

Need to check cigar

Is it possible to add one function to check cigar length == sequence length before samtools calmd, or sometimes it report error

It seems come from this situation: _N_N*
so it will divide into 3 parts. the read sequence of the second part will include the sequence of third part. Need to trim off.