10 Commits

Author	SHA1	Message	Date
Heng Li	fce87ce7bd	r121: output QUAL and unmapped to SAM	2017-06-30 14:40:54 -04:00
Heng Li	d11049eb32	r120: use max-scoring seg to control output ... much better now	2017-06-30 14:21:44 -04:00
Heng Li	1a903486b9	r118: bugfix - regs unsorted before filtering	2017-06-30 12:52:28 -04:00
Heng Li	52b4d8e2c9	r115: set primary tag; still buggy	2017-06-29 23:48:35 -04:00
Heng Li	c4871f380c	r114: make SAM output better	2017-06-29 23:08:41 -04:00
Heng Li	11167f511b	r112: output z-drop	2017-06-29 22:08:46 -04:00
Heng Li	4cd456b9ba	r108: refactoring, move reg1 routines to hit.c	2017-06-29 19:44:11 -04:00
Heng Li	4b8e88a5f4	use long options	2017-06-26 12:31:36 -04:00
Heng Li	b1077ff14c	sam output	2017-06-25 22:05:20 -04:00
Heng Li	39083be9ab	separated formating printing ... for SAM in future; and for performance	2017-06-25 16:13:54 -04:00