BAM file parsing for Ruby using C++ Bamtools library.
This gem has been created to be used in Transrate with the idea of extracting specific bits of information from a BAM file and returning it to Ruby aggregated by sequence.
Currently the information that is going to be extracted from the BAM file for each sequence is:
- number of bases mapped to each sequence
- total edit distance (from the NM tag in the BAM file)
- number of reads mapped
- number of pairs mapped
- number of pairs mapped concordantly
- number of pairs that map to different sequences and support scaffolding