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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Mon, 14 Dec 2009 13:56:40 +0000 (13:56 +0000)]
added BGB_list
git-svn-id: http://biopieces.googlecode.com/svn/trunk@806
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martinahansen [Mon, 14 Dec 2009 09:01:36 +0000 (09:01 +0000)]
renaming BBrowser to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@805
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martinahansen [Mon, 14 Dec 2009 08:58:40 +0000 (08:58 +0000)]
replacing Bbrowser with BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@804
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martinahansen [Mon, 14 Dec 2009 08:28:45 +0000 (08:28 +0000)]
added kiss_intersect
git-svn-id: http://biopieces.googlecode.com/svn/trunk@803
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martinahansen [Fri, 11 Dec 2009 19:07:17 +0000 (19:07 +0000)]
fixed bug in translate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@802
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martinahansen [Thu, 10 Dec 2009 14:58:04 +0000 (14:58 +0000)]
fixed bug in uploader
git-svn-id: http://biopieces.googlecode.com/svn/trunk@801
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martinahansen [Thu, 10 Dec 2009 14:15:13 +0000 (14:15 +0000)]
fixed bug in upload_to_bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@800
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martinahansen [Tue, 8 Dec 2009 14:42:36 +0000 (14:42 +0000)]
added security to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@799
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martinahansen [Tue, 8 Dec 2009 14:21:21 +0000 (14:21 +0000)]
added read_ace
git-svn-id: http://biopieces.googlecode.com/svn/trunk@798
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martinahansen [Tue, 8 Dec 2009 13:26:55 +0000 (13:26 +0000)]
added login to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@796
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martinahansen [Fri, 4 Dec 2009 14:52:34 +0000 (14:52 +0000)]
added file_md5 routine to Filesys.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@795
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martinahansen [Thu, 3 Dec 2009 10:58:55 +0000 (10:58 +0000)]
added space between liniea track elements
git-svn-id: http://biopieces.googlecode.com/svn/trunk@794
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martinahansen [Thu, 3 Dec 2009 10:52:28 +0000 (10:52 +0000)]
fixed inline PNG in Bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@793
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martinahansen [Wed, 2 Dec 2009 12:08:13 +0000 (12:08 +0000)]
implemented search function in bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@792
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martinahansen [Tue, 1 Dec 2009 15:13:33 +0000 (15:13 +0000)]
added DB.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@791
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martinahansen [Tue, 1 Dec 2009 15:13:18 +0000 (15:13 +0000)]
added DB.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@790
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martinahansen [Tue, 1 Dec 2009 13:38:12 +0000 (13:38 +0000)]
set bbrowser and GFF to 0-base
git-svn-id: http://biopieces.googlecode.com/svn/trunk@789
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martinahansen [Tue, 1 Dec 2009 10:59:03 +0000 (10:59 +0000)]
fixed IO rename in write_kiss
git-svn-id: http://biopieces.googlecode.com/svn/trunk@787
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martinahansen [Tue, 1 Dec 2009 10:19:09 +0000 (10:19 +0000)]
rename mistake fix2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@786
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martinahansen [Tue, 1 Dec 2009 10:18:46 +0000 (10:18 +0000)]
rename mistake fix1
git-svn-id: http://biopieces.googlecode.com/svn/trunk@785
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martinahansen [Tue, 1 Dec 2009 10:17:08 +0000 (10:17 +0000)]
renamed KISS browser to Biopiece browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@784
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martinahansen [Fri, 27 Nov 2009 15:00:37 +0000 (15:00 +0000)]
added dna export to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@782
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martinahansen [Fri, 27 Nov 2009 09:46:06 +0000 (09:46 +0000)]
changes to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@781
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martinahansen [Thu, 26 Nov 2009 13:42:51 +0000 (13:42 +0000)]
cleaned BBrowser::Tracks.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@780
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martinahansen [Thu, 26 Nov 2009 12:57:52 +0000 (12:57 +0000)]
Cleaned BBrowser::Draw
git-svn-id: http://biopieces.googlecode.com/svn/trunk@779
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martinahansen [Thu, 26 Nov 2009 12:51:35 +0000 (12:51 +0000)]
cleaned KISS.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@778
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martinahansen [Thu, 26 Nov 2009 12:37:36 +0000 (12:37 +0000)]
finished cleaning index.cgi
git-svn-id: http://biopieces.googlecode.com/svn/trunk@777
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martinahansen [Thu, 26 Nov 2009 12:30:19 +0000 (12:30 +0000)]
removed KISS directory
git-svn-id: http://biopieces.googlecode.com/svn/trunk@776
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martinahansen [Thu, 26 Nov 2009 11:38:50 +0000 (11:38 +0000)]
www relayout
git-svn-id: http://biopieces.googlecode.com/svn/trunk@775
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martinahansen [Thu, 26 Nov 2009 11:37:47 +0000 (11:37 +0000)]
www relayout
git-svn-id: http://biopieces.googlecode.com/svn/trunk@774
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martinahansen [Wed, 25 Nov 2009 20:16:24 +0000 (20:16 +0000)]
more KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@773
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martinahansen [Wed, 25 Nov 2009 15:02:46 +0000 (15:02 +0000)]
fixed color palette in KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@772
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martinahansen [Wed, 25 Nov 2009 13:40:29 +0000 (13:40 +0000)]
fixed KISS browser genome selection
git-svn-id: http://biopieces.googlecode.com/svn/trunk@771
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martinahansen [Tue, 24 Nov 2009 19:44:23 +0000 (19:44 +0000)]
fixed comma bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@770
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martinahansen [Tue, 24 Nov 2009 17:26:35 +0000 (17:26 +0000)]
kiss_sort()
git-svn-id: http://biopieces.googlecode.com/svn/trunk@769
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martinahansen [Tue, 24 Nov 2009 17:20:50 +0000 (17:20 +0000)]
fixed KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@768
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martinahansen [Tue, 24 Nov 2009 13:11:00 +0000 (13:11 +0000)]
rewrote upload_to_KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@767
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martinahansen [Tue, 24 Nov 2009 11:19:17 +0000 (11:19 +0000)]
major work on KISS browser completed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@766
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martinahansen [Mon, 16 Nov 2009 10:47:11 +0000 (10:47 +0000)]
hacked read_soft to deal with soft_files wo platform table
git-svn-id: http://biopieces.googlecode.com/svn/trunk@762
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martinahansen [Mon, 16 Nov 2009 07:39:44 +0000 (07:39 +0000)]
misc changes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@760
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martinahansen [Fri, 13 Nov 2009 10:03:31 +0000 (10:03 +0000)]
write_kiss now do blast output
git-svn-id: http://biopieces.googlecode.com/svn/trunk@759
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martinahansen [Mon, 9 Nov 2009 14:15:46 +0000 (14:15 +0000)]
added analyze_snp
git-svn-id: http://biopieces.googlecode.com/svn/trunk@758
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martinahansen [Mon, 9 Nov 2009 12:26:57 +0000 (12:26 +0000)]
fixed SAM bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@756
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martinahansen [Mon, 9 Nov 2009 08:43:40 +0000 (08:43 +0000)]
improved SAM parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@752
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martinahansen [Thu, 5 Nov 2009 13:02:13 +0000 (13:02 +0000)]
fixed KISS align code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@748
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martinahansen [Wed, 4 Nov 2009 20:07:13 +0000 (20:07 +0000)]
corrected ALIGN implementation
git-svn-id: http://biopieces.googlecode.com/svn/trunk@747
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martinahansen [Wed, 4 Nov 2009 08:06:24 +0000 (08:06 +0000)]
fixed details in bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@743
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martinahansen [Fri, 30 Oct 2009 10:55:41 +0000 (10:55 +0000)]
added read_sam
git-svn-id: http://biopieces.googlecode.com/svn/trunk@724
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martinahansen [Thu, 29 Oct 2009 15:10:11 +0000 (15:10 +0000)]
fixed bug in patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@721
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martinahansen [Thu, 29 Oct 2009 13:52:45 +0000 (13:52 +0000)]
modified split_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@718
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martinahansen [Thu, 29 Oct 2009 10:46:50 +0000 (10:46 +0000)]
corrected error message in dir_create
git-svn-id: http://biopieces.googlecode.com/svn/trunk@715
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martinahansen [Wed, 28 Oct 2009 17:19:29 +0000 (17:19 +0000)]
KISS browser working, but slow
git-svn-id: http://biopieces.googlecode.com/svn/trunk@714
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martinahansen [Wed, 28 Oct 2009 09:30:09 +0000 (09:30 +0000)]
added ALIGN view support to KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@713
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martinahansen [Tue, 27 Oct 2009 17:02:09 +0000 (17:02 +0000)]
more work on KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@712
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martinahansen [Tue, 27 Oct 2009 07:47:58 +0000 (07:47 +0000)]
revised KISS format
git-svn-id: http://biopieces.googlecode.com/svn/trunk@710
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martinahansen [Sat, 24 Oct 2009 20:26:48 +0000 (20:26 +0000)]
added zoom and move to KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@709
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martinahansen [Fri, 23 Oct 2009 08:11:35 +0000 (08:11 +0000)]
removed jbrowse support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@708
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martinahansen [Thu, 22 Oct 2009 07:10:50 +0000 (07:10 +0000)]
KISS upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@707
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martinahansen [Thu, 22 Oct 2009 05:48:35 +0000 (05:48 +0000)]
added www
git-svn-id: http://biopieces.googlecode.com/svn/trunk@706
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martinahansen [Wed, 21 Oct 2009 19:03:54 +0000 (19:03 +0000)]
changed KISS format
git-svn-id: http://biopieces.googlecode.com/svn/trunk@705
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martinahansen [Wed, 21 Oct 2009 16:43:09 +0000 (16:43 +0000)]
added upload_to_KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@703
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martinahansen [Wed, 21 Oct 2009 14:34:27 +0000 (14:34 +0000)]
added kiss biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@701
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martinahansen [Wed, 21 Oct 2009 06:04:03 +0000 (06:04 +0000)]
fixed dna/DNA bug in Align.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@699
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martinahansen [Mon, 19 Oct 2009 13:28:17 +0000 (13:28 +0000)]
added XHTML
git-svn-id: http://biopieces.googlecode.com/svn/trunk@698
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martinahansen [Sun, 18 Oct 2009 18:40:59 +0000 (18:40 +0000)]
added write_gff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@696
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martinahansen [Sat, 17 Oct 2009 10:58:15 +0000 (10:58 +0000)]
renaming create_blast_db to create_blast_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@694
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martinahansen [Sat, 17 Oct 2009 10:39:09 +0000 (10:39 +0000)]
changed options in create_blast_db
git-svn-id: http://biopieces.googlecode.com/svn/trunk@690
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martinahansen [Wed, 30 Sep 2009 07:55:35 +0000 (07:55 +0000)]
fixed bug in get_genome_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@688
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martinahansen [Tue, 29 Sep 2009 08:44:46 +0000 (08:44 +0000)]
fixed STRAND in SAM format
git-svn-id: http://biopieces.googlecode.com/svn/trunk@687
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martinahansen [Mon, 28 Sep 2009 16:35:07 +0000 (16:35 +0000)]
added SAM.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@686
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martinahansen [Mon, 28 Sep 2009 16:29:54 +0000 (16:29 +0000)]
added bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@685
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martinahansen [Mon, 21 Sep 2009 15:32:40 +0000 (15:32 +0000)]
added assemble_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@682
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martinahansen [Mon, 21 Sep 2009 07:56:31 +0000 (07:56 +0000)]
added format to compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@681
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martinahansen [Mon, 21 Sep 2009 07:21:16 +0000 (07:21 +0000)]
cleaned up calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@679
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martinahansen [Fri, 18 Sep 2009 08:42:41 +0000 (08:42 +0000)]
added features to calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@677
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martinahansen [Fri, 18 Sep 2009 08:11:32 +0000 (08:11 +0000)]
added strand to assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@675
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martinahansen [Fri, 18 Sep 2009 06:27:40 +0000 (06:27 +0000)]
added ugly hack to assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@673
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martinahansen [Fri, 18 Sep 2009 06:14:33 +0000 (06:14 +0000)]
added align_two_seq.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@672
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martinahansen [Fri, 18 Sep 2009 06:12:45 +0000 (06:12 +0000)]
fixed issue 18
git-svn-id: http://biopieces.googlecode.com/svn/trunk@671
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martinahansen [Thu, 17 Sep 2009 16:17:28 +0000 (16:17 +0000)]
added get_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@669
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martinahansen [Wed, 16 Sep 2009 07:47:39 +0000 (07:47 +0000)]
fixed match_seq bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@668
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martinahansen [Wed, 9 Sep 2009 09:00:38 +0000 (09:00 +0000)]
fixed bug in psl2bed conversion
git-svn-id: http://biopieces.googlecode.com/svn/trunk@666
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martinahansen [Wed, 9 Sep 2009 06:53:23 +0000 (06:53 +0000)]
fixed wrap blunder in Fasta.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@665
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martinahansen [Wed, 9 Sep 2009 06:48:29 +0000 (06:48 +0000)]
added BED entry output to check_bed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@664
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martinahansen [Tue, 8 Sep 2009 08:15:50 +0000 (08:15 +0000)]
added BWA index support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@662
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martinahansen [Tue, 8 Sep 2009 07:12:59 +0000 (07:12 +0000)]
unfucked bowtie_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@661
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martinahansen [Tue, 8 Sep 2009 07:09:04 +0000 (07:09 +0000)]
fuckup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@660
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martinahansen [Mon, 7 Sep 2009 18:53:40 +0000 (18:53 +0000)]
sanitized create_bowtie_index code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@659
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martinahansen [Mon, 7 Sep 2009 18:33:19 +0000 (18:33 +0000)]
sanitized create_bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@658
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martinahansen [Mon, 7 Sep 2009 11:07:47 +0000 (11:07 +0000)]
fixed solexa/phred code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@654
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martinahansen [Fri, 4 Sep 2009 15:05:29 +0000 (15:05 +0000)]
changed options of read_solexa and read_fastq - undocumented
git-svn-id: http://biopieces.googlecode.com/svn/trunk@653
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martinahansen [Fri, 4 Sep 2009 14:33:25 +0000 (14:33 +0000)]
added mate_pair_dist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@652
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martinahansen [Fri, 4 Sep 2009 14:32:01 +0000 (14:32 +0000)]
disabled quality score conversion in FASTQ and Solexa
git-svn-id: http://biopieces.googlecode.com/svn/trunk@650
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martinahansen [Wed, 2 Sep 2009 10:20:14 +0000 (10:20 +0000)]
fixed issues in fastq handling
git-svn-id: http://biopieces.googlecode.com/svn/trunk@648
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Fri, 28 Aug 2009 11:26:54 +0000 (11:26 +0000)]
more work on AlignTwoSeq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@647
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 27 Aug 2009 15:05:05 +0000 (15:05 +0000)]
working on AlignTwoSeq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@645
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 25 Aug 2009 10:53:29 +0000 (10:53 +0000)]
fixed cpu switch in bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@644
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 20 Aug 2009 12:57:01 +0000 (12:57 +0000)]
finished rescan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@642
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 20 Aug 2009 06:37:07 +0000 (06:37 +0000)]
added more range to plot_lendist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@640
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 18 Aug 2009 09:59:12 +0000 (09:59 +0000)]
updated rescan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@638
74ccb610-7750-0410-82ae-
013aeee3265d
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