lh3/seqtk — pull request #33 by kdmurray91 (2014-08-07 10:06:33+00:00)
Title: CLI option to remove adaptor sequence from read sequence

This implements a CLI flag to actually remove the adapter sequence from
the read's sequence, instead of just masking it out. The quality string
is correctly removed also.

To do so, we null-terminate the `kseq_t`'s qual and seq `char *`s at the correct length for 3' adapters, or `strncpy`s the read's true sequence (&qual string) to the start of the `char *`, copying the null byte.
In both cases, the lengths of seq and qual are updated.

Cheers for yet another awesome tool!

K