8 Commits

Include renames

Author	SHA1	Message	Date
Heng Li	24a4808826	r718: retrieve sequence from the index	2018-02-23 10:18:26 -05:00
Heng Li	1372977a37	r708: implemented double Z-drop thresholds (#112) ... When aligning long reads, we would prefer to align through low-quality regions. This requires a large Z-drop threshold. However, to find small inversions, we need to use a small Z-drop. This commit address this conflict with two Z-drop thresholds. When Z-drop exceeds the smaller threshold, we perform a local alignment to check if there is a potential inversion. If there is one, we break the alignment; otherwise we break the alignment only if Z-drop excess the larger threshold. This commit also fixes a bug that reported wrong coordinates when the inversion is on the forward strand (#112).	2018-02-15 10:50:49 -05:00
Heng Li	7ef5490884	r703: added --max-clip-ratio ... still testing the option	2018-02-12 13:29:18 -05:00
Heng Li	29b4a1786c	r685: tune end seed filter again	2018-02-05 11:48:22 -05:00
Heng Li	dbf284b2d9	r684: separate end score from min_chain_score	2018-02-05 11:40:38 -05:00
Heng Li	da6947cfa3	r671: cleanup command line options	2018-01-31 13:59:52 -05:00
Heng Li	d676a5314b	r664: use --heat-sort for sr by default	2018-01-26 12:25:42 -05:00
Heng Li	123bc1d91d	put option operations in another file	2018-01-26 08:38:37 -05:00