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git.donarmstrong.com Git - biopieces.git/log
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
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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
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martinahansen [Mon, 8 Jun 2009 20:30:11 +0000 (20:30 +0000)]
rewrote bioscript
git-svn-id: http://biopieces.googlecode.com/svn/trunk@517
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martinahansen [Mon, 8 Jun 2009 20:11:59 +0000 (20:11 +0000)]
rewrote bioscript
git-svn-id: http://biopieces.googlecode.com/svn/trunk@514
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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
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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
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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
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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
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martinahansen [Sat, 6 Jun 2009 16:42:00 +0000 (16:42 +0000)]
implementing status solution
git-svn-id: http://biopieces.googlecode.com/svn/trunk@488
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martinahansen [Sat, 6 Jun 2009 15:40:49 +0000 (15:40 +0000)]
removed variables bulk type
git-svn-id: http://biopieces.googlecode.com/svn/trunk@487
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martinahansen [Sat, 6 Jun 2009 15:22:43 +0000 (15:22 +0000)]
fixing status
git-svn-id: http://biopieces.googlecode.com/svn/trunk@486
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martinahansen [Fri, 5 Jun 2009 17:20:28 +0000 (17:20 +0000)]
added align_pair_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@485
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martinahansen [Fri, 5 Jun 2009 09:00:45 +0000 (09:00 +0000)]
migration done
git-svn-id: http://biopieces.googlecode.com/svn/trunk@484
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martinahansen [Fri, 5 Jun 2009 08:54:29 +0000 (08:54 +0000)]
almost done
git-svn-id: http://biopieces.googlecode.com/svn/trunk@482
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martinahansen [Fri, 5 Jun 2009 08:03:41 +0000 (08:03 +0000)]
migrated removers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@480
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martinahansen [Fri, 5 Jun 2009 07:30:14 +0000 (07:30 +0000)]
migrated upload_to_ucsc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@477
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martinahansen [Thu, 4 Jun 2009 19:14:37 +0000 (19:14 +0000)]
almost there
git-svn-id: http://biopieces.googlecode.com/svn/trunk@475
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martinahansen [Thu, 4 Jun 2009 15:34:51 +0000 (15:34 +0000)]
fixed a couple of bugs - good
git-svn-id: http://biopieces.googlecode.com/svn/trunk@474
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martinahansen [Thu, 4 Jun 2009 13:43:56 +0000 (13:43 +0000)]
fixed bug in sort_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@473
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martinahansen [Tue, 2 Jun 2009 18:37:28 +0000 (18:37 +0000)]
bleh blah
git-svn-id: http://biopieces.googlecode.com/svn/trunk@472
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martinahansen [Tue, 2 Jun 2009 18:09:33 +0000 (18:09 +0000)]
deleting read_phastcons
git-svn-id: http://biopieces.googlecode.com/svn/trunk@470
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martinahansen [Tue, 2 Jun 2009 16:48:32 +0000 (16:48 +0000)]
remove bin dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@468
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martinahansen [Tue, 2 Jun 2009 15:14:14 +0000 (15:14 +0000)]
3 more again
git-svn-id: http://biopieces.googlecode.com/svn/trunk@467
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martinahansen [Tue, 2 Jun 2009 14:42:44 +0000 (14:42 +0000)]
3 more
git-svn-id: http://biopieces.googlecode.com/svn/trunk@464
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martinahansen [Tue, 2 Jun 2009 12:34:05 +0000 (12:34 +0000)]
more read_ tools migrated
git-svn-id: http://biopieces.googlecode.com/svn/trunk@462
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martinahansen [Tue, 2 Jun 2009 12:17:53 +0000 (12:17 +0000)]
migrating read_ tools
git-svn-id: http://biopieces.googlecode.com/svn/trunk@460
74ccb610-7750-0410-82ae-
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projects / biopieces.git / log