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git.donarmstrong.com Git - biopieces.git/log
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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martinahansen [Sun, 12 Jul 2009 20:52:48 +0000 (20:52 +0000)]
more ruby stuff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@566
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martinahansen [Sat, 11 Jul 2009 13:39:19 +0000 (13:39 +0000)]
fixed bug in read_embl
git-svn-id: http://biopieces.googlecode.com/svn/trunk@565
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martinahansen [Fri, 10 Jul 2009 18:38:43 +0000 (18:38 +0000)]
speedup of analyze_seq 3 fold
git-svn-id: http://biopieces.googlecode.com/svn/trunk@564
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martinahansen [Fri, 10 Jul 2009 16:47:52 +0000 (16:47 +0000)]
added str_analyze to Common.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@563
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martinahansen [Fri, 10 Jul 2009 15:07:59 +0000 (15:07 +0000)]
fixed bug in create_vmatch_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@562
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martinahansen [Fri, 10 Jul 2009 14:36:04 +0000 (14:36 +0000)]
fixed bug in remove_indels
git-svn-id: http://biopieces.googlecode.com/svn/trunk@561
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martinahansen [Fri, 10 Jul 2009 12:53:03 +0000 (12:53 +0000)]
mucking with c and makefiles
git-svn-id: http://biopieces.googlecode.com/svn/trunk@560
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martinahansen [Wed, 8 Jul 2009 09:22:22 +0000 (09:22 +0000)]
use warnings added to perl modules
git-svn-id: http://biopieces.googlecode.com/svn/trunk@559
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martinahansen [Wed, 8 Jul 2009 09:10:21 +0000 (09:10 +0000)]
added use strict to all biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@558
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martinahansen [Wed, 8 Jul 2009 08:47:04 +0000 (08:47 +0000)]
changed shebang
git-svn-id: http://biopieces.googlecode.com/svn/trunk@557
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martinahansen [Tue, 7 Jul 2009 20:24:39 +0000 (20:24 +0000)]
minor changes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@556
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martinahansen [Sat, 4 Jul 2009 14:02:37 +0000 (14:02 +0000)]
updated seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@554
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martinahansen [Fri, 3 Jul 2009 15:08:59 +0000 (15:08 +0000)]
last cleanups
git-svn-id: http://biopieces.googlecode.com/svn/trunk@553
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martinahansen [Fri, 3 Jul 2009 14:40:18 +0000 (14:40 +0000)]
clearning ruby dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@552
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martinahansen [Wed, 1 Jul 2009 10:17:11 +0000 (10:17 +0000)]
changed seq_type from string to symbols in ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@551
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martinahansen [Wed, 1 Jul 2009 10:11:34 +0000 (10:11 +0000)]
changed seq_type from string to symbols in ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@550
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martinahansen [Tue, 30 Jun 2009 20:33:33 +0000 (20:33 +0000)]
updated ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@549
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martinahansen [Tue, 30 Jun 2009 20:19:36 +0000 (20:19 +0000)]
cleanded up test_seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@548
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martinahansen [Tue, 30 Jun 2009 18:39:51 +0000 (18:39 +0000)]
added unit testing for ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@547
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martinahansen [Tue, 30 Jun 2009 17:03:36 +0000 (17:03 +0000)]
added unit testing for ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@546
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martinahansen [Tue, 30 Jun 2009 17:01:34 +0000 (17:01 +0000)]
added unit testing for ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@545
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martinahansen [Mon, 29 Jun 2009 19:15:32 +0000 (19:15 +0000)]
added seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@544
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martinahansen [Tue, 23 Jun 2009 10:36:40 +0000 (10:36 +0000)]
fixes and stuff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@541
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martinahansen [Wed, 17 Jun 2009 11:09:22 +0000 (11:09 +0000)]
fixed a number of bugs in PSL
git-svn-id: http://biopieces.googlecode.com/svn/trunk@539
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martinahansen [Tue, 16 Jun 2009 11:56:34 +0000 (11:56 +0000)]
fixed perl5.10 issue for soft parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@535
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martinahansen [Tue, 16 Jun 2009 10:08:17 +0000 (10:08 +0000)]
added VMATCH support to get_genome_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@534
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martinahansen [Tue, 16 Jun 2009 07:19:29 +0000 (07:19 +0000)]
fixed bug in time_stamp_diff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@532
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martinahansen [Mon, 15 Jun 2009 18:19:52 +0000 (18:19 +0000)]
added indel_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@531
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martinahansen [Mon, 15 Jun 2009 17:13:24 +0000 (17:13 +0000)]
added mutate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@527
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martinahansen [Mon, 15 Jun 2009 15:31:30 +0000 (15:31 +0000)]
added non-overlapping feature to split_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@525
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martinahansen [Mon, 15 Jun 2009 14:13:56 +0000 (14:13 +0000)]
fixed bug in Fasta.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@524
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martinahansen [Thu, 11 Jun 2009 13:37:46 +0000 (13:37 +0000)]
added Data::Dumper support to bioscript
git-svn-id: http://biopieces.googlecode.com/svn/trunk@522
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martinahansen [Tue, 9 Jun 2009 10:48:19 +0000 (10:48 +0000)]
fixed bug in plot_histogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@519
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 9 Jun 2009 10:46:18 +0000 (10:46 +0000)]
fixed bug in read_tab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@518
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 8 Jun 2009 20:30:11 +0000 (20:30 +0000)]
rewrote bioscript
git-svn-id: http://biopieces.googlecode.com/svn/trunk@517
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 8 Jun 2009 20:11:59 +0000 (20:11 +0000)]
rewrote bioscript
git-svn-id: http://biopieces.googlecode.com/svn/trunk@514
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 8 Jun 2009 13:53:54 +0000 (13:53 +0000)]
fixed minor bugs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@513
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Sat, 6 Jun 2009 20:40:44 +0000 (20:40 +0000)]
fixed bug in format_genome
git-svn-id: http://biopieces.googlecode.com/svn/trunk@496
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Sat, 6 Jun 2009 18:16:30 +0000 (18:16 +0000)]
fixes but in removal of tmp_dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@491
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Sat, 6 Jun 2009 17:27:31 +0000 (17:27 +0000)]
fixes done to tmp_dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@489
74ccb610-7750-0410-82ae-
013aeee3265d
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