najoshi/sickle — pull request #27 by biocyberman (2014-05-09 15:42:24+00:00)
Title: Tuned sliding.c and added support for colorspace

Hi,
Thanks for sharing `sickle`.

I did some tuning of sliding.c in efc18a4 commit, and added support for colorspace in cc02945 commit. The new sliding.c will first try to identify five_prime_cut and three_prime_cut and ignore -x flag at this stage. When the two cut point are found, then it start considering -x flag and reset five_prime_cut. I also made small adjustment on three_prime_cut initialization (to 'fqrec->qual.l - 1' instead of fqrec->seq.l).

In trim_single.c I added option to cope with base sequence prefix in color-space sequence. And when this option is used, `sickle` disables five_prime_cut when printing output.