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git.donarmstrong.com Git - biopieces.git/log
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
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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
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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
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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
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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
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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
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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
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martinahansen [Fri, 14 Aug 2009 16:35:06 +0000 (16:35 +0000)]
added rescan_seq Restriction Enzyme scanner
git-svn-id: http://biopieces.googlecode.com/svn/trunk@636
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martinahansen [Fri, 14 Aug 2009 16:07:25 +0000 (16:07 +0000)]
polished RestrictEnz.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@635
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martinahansen [Fri, 14 Aug 2009 15:37:38 +0000 (15:37 +0000)]
added RestrictEnz.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@634
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martinahansen [Wed, 12 Aug 2009 13:44:11 +0000 (13:44 +0000)]
added analyze_gc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@633
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martinahansen [Mon, 10 Aug 2009 16:03:26 +0000 (16:03 +0000)]
added nifty # detail to read_tab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@631
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martinahansen [Mon, 10 Aug 2009 08:30:27 +0000 (08:30 +0000)]
added --logscale_y switch to relevant plot_* biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@628
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martinahansen [Mon, 10 Aug 2009 07:31:17 +0000 (07:31 +0000)]
disabled utest for C code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@627
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martinahansen [Mon, 10 Aug 2009 07:25:31 +0000 (07:25 +0000)]
added --no_gaps switch in blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@625
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martinahansen [Tue, 4 Aug 2009 15:20:57 +0000 (15:20 +0000)]
added a skip_scores switch to read_solexa and read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@624
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martinahansen [Sun, 2 Aug 2009 19:01:53 +0000 (19:01 +0000)]
fix embl parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@623
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martinahansen [Sun, 2 Aug 2009 10:58:48 +0000 (10:58 +0000)]
finishing read_embl
git-svn-id: http://biopieces.googlecode.com/svn/trunk@620
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martinahansen [Sun, 2 Aug 2009 08:32:24 +0000 (08:32 +0000)]
added get_embl_entry
git-svn-id: http://biopieces.googlecode.com/svn/trunk@615
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martinahansen [Wed, 29 Jul 2009 14:21:54 +0000 (14:21 +0000)]
added embl_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@614
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martinahansen [Wed, 29 Jul 2009 08:48:03 +0000 (08:48 +0000)]
added .biopiecesrc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@612
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martinahansen [Tue, 28 Jul 2009 17:31:55 +0000 (17:31 +0000)]
finished write_mysql
git-svn-id: http://biopieces.googlecode.com/svn/trunk@607
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martinahansen [Tue, 28 Jul 2009 14:00:24 +0000 (14:00 +0000)]
changed read_solexa
git-svn-id: http://biopieces.googlecode.com/svn/trunk@605
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martinahansen [Tue, 28 Jul 2009 08:02:15 +0000 (08:02 +0000)]
added quality threshold to read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@603
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martinahansen [Mon, 27 Jul 2009 22:01:43 +0000 (22:01 +0000)]
added write_mysql
git-svn-id: http://biopieces.googlecode.com/svn/trunk@601
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martinahansen [Mon, 27 Jul 2009 16:51:39 +0000 (16:51 +0000)]
fixed list_mysql_databases
git-svn-id: http://biopieces.googlecode.com/svn/trunk@598
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martinahansen [Mon, 27 Jul 2009 10:47:37 +0000 (10:47 +0000)]
added list_mysql_databases
git-svn-id: http://biopieces.googlecode.com/svn/trunk@597
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martinahansen [Sat, 25 Jul 2009 08:45:37 +0000 (08:45 +0000)]
fixed feature in analyze_vals, issue 3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@595
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martinahansen [Fri, 24 Jul 2009 08:33:18 +0000 (08:33 +0000)]
fixed Gwiki colors
git-svn-id: http://biopieces.googlecode.com/svn/trunk@594
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martinahansen [Thu, 23 Jul 2009 19:17:16 +0000 (19:17 +0000)]
fixed bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@593
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martinahansen [Thu, 23 Jul 2009 14:07:04 +0000 (14:07 +0000)]
fixed bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@588
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martinahansen [Thu, 23 Jul 2009 13:29:45 +0000 (13:29 +0000)]
added Bowtie.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@586
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martinahansen [Thu, 23 Jul 2009 13:23:20 +0000 (13:23 +0000)]
added create_bowtie_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@584
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martinahansen [Thu, 23 Jul 2009 12:33:52 +0000 (12:33 +0000)]
added verbose stuff to bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@583
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martinahansen [Thu, 23 Jul 2009 11:42:25 +0000 (11:42 +0000)]
added verbose stuff to format_genome
git-svn-id: http://biopieces.googlecode.com/svn/trunk@582
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martinahansen [Thu, 23 Jul 2009 11:16:20 +0000 (11:16 +0000)]
addid term colors to list_genomes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@581
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martinahansen [Thu, 23 Jul 2009 10:25:17 +0000 (10:25 +0000)]
added options to bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@579
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martinahansen [Wed, 22 Jul 2009 08:41:19 +0000 (08:41 +0000)]
added some args to bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@577
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martinahansen [Tue, 21 Jul 2009 20:03:00 +0000 (20:03 +0000)]
added test_common.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@576
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martinahansen [Tue, 21 Jul 2009 11:36:31 +0000 (11:36 +0000)]
fixed bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@574
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martinahansen [Tue, 21 Jul 2009 08:50:52 +0000 (08:50 +0000)]
added read_fastq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@572
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martinahansen [Mon, 20 Jul 2009 21:44:23 +0000 (21:44 +0000)]
added bowtie_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@570
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martinahansen [Mon, 20 Jul 2009 14:18:28 +0000 (14:18 +0000)]
added bowtie to format_genome
git-svn-id: http://biopieces.googlecode.com/svn/trunk@568
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martinahansen [Sun, 19 Jul 2009 19:20:18 +0000 (19:20 +0000)]
adding to ruby source
git-svn-id: http://biopieces.googlecode.com/svn/trunk@567
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