Improvements: short reads

[nlapalu]

Dear @lfaino

Do you think it would be difficult to implement an option to use several bam files for short reads (many libs), instead of merging in a very huge file. Or another solution (very interesting for me !), an option to provide many libs of assembled transcripts (avoiding transcript assembly).

Thanks nico.

[lfaino]

very nice suggestion. once i tried to implement it but i should pick up the option