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634 Commits (5fc0f44e2760040938a2bddc6f14bd79541b04e4)

Author SHA1 Message Date
Heng Li 5fc0f44e27 mapQ is not quite right 2014-09-19 23:39:59 -04:00
Heng Li a33ca20499 separate postalt to a separate script 2014-09-19 23:23:54 -04:00
Heng Li 23bc50e240 removed altlift; suppress primary hit by default 2014-09-19 17:05:27 -04:00
Heng Li 7426a750ec r868: use soft clip for ALT hits 2014-09-19 16:58:18 -04:00
Heng Li 9af36064e8 r867: fixed a few bugs; added ALT hits to XA 2014-09-19 16:50:21 -04:00
Heng Li b22bed2b5e removed <> from markdown 2014-09-18 11:54:23 -04:00
Heng Li 030825ae85 updated release notes 2014-09-18 11:51:52 -04:00
Heng Li ba7ed47d40 error in altpost 2014-09-18 11:18:10 -04:00
Heng Li a41afe4c97 These files were committed on a wrong branch 2014-09-18 10:49:35 -04:00
Heng Li a32d44d8d6 r855: show ALT hits in the PE mode, too 
In the previous version, it does not
 2014-09-17 23:07:56 -04:00
Heng Li c982443210 r854: improved the calculation of pa 
and build pa filtering into BWA-MEM
 2014-09-17 16:26:28 -04:00
Heng Li f5a0e576e6 added postalt to bwa-helper for post processing 2014-09-17 14:18:40 -04:00
Heng Li 825ae92e58 r849: the pa tag now gives a number 
... which is the ratio of this hit to the best ALT hit.
 2014-09-17 13:05:35 -04:00
Heng Li 6f37c14f26 r848: tag alignments with primary ALT 2014-09-16 18:52:49 -04:00
Heng Li a458442b24 r845: updated NEWS 
I will use the new version for a while and then release it.
 2014-09-16 14:38:41 -04:00
Heng Li 92bc6849a3 r844: added intra-species contig mapping mode 2014-09-16 10:53:07 -04:00
Heng Li 90518f11e3 r843: presetting for ONT 2d reads 
Somewhat working for 1d reads, but not very well
 2014-09-16 10:38:15 -04:00
Heng Li 230cd16712 updated dependency 2014-09-16 10:17:30 -04:00
Heng Li d0af3648d1 Fixed a typo 2014-09-16 10:16:45 -04:00
Heng Li 43ce69104d Removed PacBio read-to-read instruction 2014-09-15 23:59:35 -04:00
Heng Li d013ea94b0 Removed instruction on ALT alignment 
Favoring the new method
 2014-09-15 23:45:17 -04:00
Heng Li 4b6eeb34c8 r830: optionally fixed chunk size 2014-09-15 23:42:24 -04:00
Heng Li 624687b072 r829: killed a harmless gcc warning 2014-09-15 23:33:22 -04:00
Heng Li 5d26ab0ee3 r828: changed the default scoring for pacbio 2014-09-15 23:22:05 -04:00
Heng Li b07587f806 r827: an alt hit as good as a pri hit as supp 2014-09-15 16:07:51 -04:00
Heng Li bd85af08ab r826: improved alt mapping for PE 2014-09-15 12:13:04 -04:00
Heng Li aee53f1334 r824: ALT mapping seems working 2014-09-15 00:29:05 -04:00
Heng Li 015ab3f6c3 r823: towards ALT support 2014-09-14 16:41:14 -04:00
Heng Li 8116bcc786 Merge branch 'dev' into alt 2014-09-14 15:40:52 -04:00
Heng Li 8d2b93156b r821: more relax on containing seeds 2014-09-12 10:35:49 -04:00
Heng Li 6739b713dd Merge branch 'hotfix-utgaln' into dev 
Conflicts:
	main.c
 2014-09-08 12:44:42 -04:00
Heng Li f4aedddee6 r819: bugfix - added too many sub-SMEMs 2014-09-08 11:32:48 -04:00
Heng Li ca61fe3ad5 code backup 2014-09-08 08:52:02 -04:00
Heng Li 1934f0cf24 code backup 2014-09-05 13:20:52 -04:00
Heng Li e4ad616d43 r816: read .alt file (not tested) 2014-09-05 12:49:50 -04:00
Heng Li 35ac99b4f7 r815: optionally output ref fasta header 
Also fixed a bug in reading .ann files
 2014-08-29 10:51:23 -04:00
Heng Li 1e611b235c r810: add err_puts() 
puts() adds '\n', but fputs() does not.
 2014-08-26 11:07:24 -04:00
Heng Li b5cba257c1 r809: new strategy for the -a mode 2014-08-25 11:59:27 -04:00
Heng Li bf7d1d46ca r808: a minor bug with the new index -b 2014-08-25 10:36:24 -04:00
Heng Li 1bba5ef20e r807: allow to change block size in bwt_gen 
For a very large reference genome, the default is too small.
 2014-08-25 10:31:54 -04:00
Heng Li b73f4c977a Merge branch 'master' into new-master 2014-08-07 21:51:58 -04:00
Mustafa Ozdal 0a6f2660b4 Fixed a bug related to the score returned. 2014-08-07 13:50:42 -07:00
Mustafa Ozdal c1df343740 Merge branch 'master' of github.com:lh3/bwa 2014-08-07 13:49:01 -07:00
Heng Li 9bdcf31dec don't process hard clipped SEQ 
The full read sequence has to be present.
 2014-08-07 13:48:51 -07:00
Heng Li a1a57d97be r796: more debugging code 2014-08-07 14:58:51 -04:00
Heng Li d9dfab2ba2 r795: intel's ksw_extend() replacement 2014-08-07 13:43:07 -04:00
Heng Li b5415ba23d first integration; compiled, but NOT TESTED! 2014-08-07 11:59:37 -04:00
Heng Li 5e56bec0f4 don't process hard clipped SEQ 
The full read sequence has to be present.
 2014-08-07 10:36:28 -04:00
Heng Li 705aa53894 Released 0.7.10 2014-07-13 22:57:27 -04:00
Heng Li 7fd6a11569 r788: segfault when the last ref is "weird" 
mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
 2014-07-10 10:53:56 -04:00