lh3/bwa — pull request #21 by bpow (2014-01-05 20:05:44+00:00)
Title: fix duplicate PG lines in bwape and bwase

ff6faf8 introduced code to print the PG lines for `bwamem.c`. Since `bwape.c` and `bwase.c` already had code to print a PG line (albeit without CL), this resulted in duplicate @PG entries in the latter programs (which violates the unique-id requirement for PG records per the SAM spec).

This pull request just removes the older printing of the PG lines, leaving printing in place within `bwa_print_sam_hdr`.