pezmaster31/bamtools — Issue #26: An error message in split function, and a minor suggestion
Author: fyfy
Created: 2011-12-04 03:40:52+00:00
State: open

Dear Derek:
I used bamtool split function and have two comments:
1) It exits with an error message (see below) that can be avoided if I pre-filter the BAM file to remove unmapped reads:
terminate called after throwing an instance of 'std::out_of_range'
what(): vector::_M_range_check
Abort

I guess it could be faster if the 'bamtools filters -IsMapped true' can be avoided in the processing step. May I recommend to tolerate unmapped read in the split function and output the unmapped reads to a separated file as stub.unmapped.bam, if possible.

2) the default suffix after stub string is .REF_refname such as .REF_chr1. Although I can modify the code, it is useful for me to have an option to change the 'REF' to any string such as 'c'. This might not be useful for other users though.

Thanks a lot.

Fan