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993 Commits (dd7db7beb687d4ec3d0c06f815167cfeaa21a22c)

Author SHA1 Message Date
Heng Li a41afe4c97 These files were committed on a wrong branch 2014-09-18 10:49:35 -04:00
Heng Li dd1c6619d7 r858: bugfix in PE alt alignments 
Alignments found with mate rescue are not flagged with "is_alt"
 2014-09-18 10:47:21 -04:00
Heng Li b9026ecafd Merge branch 'dev' 2014-09-17 23:18:09 -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 d677a4325b Merge branch 'dev' 
Conflicts:
	main.c
 2014-09-17 14:22:20 -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 945d39fb79 Merge branch 'dev' 
Conflicts:
	main.c
 2014-09-16 14:39:33 -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 152d25ff87 Merge branch 'dev' 2014-09-16 10:17:53 -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 1bdd791539 r837: removed BAM support 
This is not necessary.
 2014-09-16 09:57:35 -04:00
Heng Li 7244d66833 r836: a dangerous merge 2014-09-16 00:37:58 -04:00
Heng Li df09f38ad3 Merge branch 'dev' 
Conflicts:
	README.md
	bwamem.c
	bwamem_pair.c
	fastmap.c
	main.c
 2014-09-16 00:24:41 -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 41b137d202 Merge pull request #32 from mmoisse/patch-1 
Update example Illumina paired-end reads
 2014-09-15 22:59:22 -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
mmoisse dfd8c9eeb6 Update README.md 
The 'Illumina paired-end reads no longer than ~70bp' example should use sampe instead of samse
 2014-09-14 11:26:39 +02:00
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 c7679ee781 Merge pull request #31 from jwbargsten/master 
wrong function to print @HD line in bwa_print_sam_hdr
 2014-08-29 10:22:11 -04:00
Joachim Bargsten 9c5fd803e9 wrong function to print @HD line in bwa_print_sam_hdr 2014-08-29 11:51:07 +02:00
Heng Li 1e611b235c r810: add err_puts() 
puts() adds '\n', but fputs() does not.
 2014-08-26 11:07:24 -04:00
Heng Li d9f654908f Merge pull request #30 from mp15/header_hd 
Add @HD tag to SAM header
 2014-08-26 09:44:29 -04:00
Martin O. Pollard ec55ed8d83 Add @HD tag to SAM header 2014-08-26 12:06:16 +01:00
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 1de61b556e r806: polish BAM support 2014-08-08 13:36:56 -04:00
Heng Li 8a230db596 Merge branch 'nh_bam_support' of git://github.com/nh13/bwa into nh13-nh_bam_support 2014-08-08 13:12:54 -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