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git.donarmstrong.com Git - biopieces.git/log
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
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martinahansen [Tue, 2 Jun 2009 11:12:26 +0000 (11:12 +0000)]
migration of all write tools done
git-svn-id: http://biopieces.googlecode.com/svn/trunk@458
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martinahansen [Tue, 2 Jun 2009 10:57:14 +0000 (10:57 +0000)]
migrated 3 write tools
git-svn-id: http://biopieces.googlecode.com/svn/trunk@457
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martinahansen [Fri, 29 May 2009 12:13:05 +0000 (12:13 +0000)]
migrated final plotters
git-svn-id: http://biopieces.googlecode.com/svn/trunk@455
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martinahansen [Fri, 29 May 2009 10:04:43 +0000 (10:04 +0000)]
migrated plot_lendist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@453
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martinahansen [Fri, 29 May 2009 09:56:36 +0000 (09:56 +0000)]
migrated plot_karyogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@450
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martinahansen [Fri, 29 May 2009 09:40:25 +0000 (09:40 +0000)]
migrated plot_histogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@449
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martinahansen [Fri, 29 May 2009 09:23:06 +0000 (09:23 +0000)]
migrated plot_chrdist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@447
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martinahansen [Thu, 28 May 2009 11:46:06 +0000 (11:46 +0000)]
migrated remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@445
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martinahansen [Thu, 28 May 2009 10:34:23 +0000 (10:34 +0000)]
migrated 4 more
git-svn-id: http://biopieces.googlecode.com/svn/trunk@442
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martinahansen [Thu, 28 May 2009 10:14:12 +0000 (10:14 +0000)]
migrated tile_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@441
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martinahansen [Thu, 28 May 2009 10:01:12 +0000 (10:01 +0000)]
migrated sort_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@438
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martinahansen [Thu, 28 May 2009 09:51:57 +0000 (09:51 +0000)]
migrated sum_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@436
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martinahansen [Thu, 28 May 2009 09:43:48 +0000 (09:43 +0000)]
migrated patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@435
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martinahansen [Thu, 28 May 2009 09:43:16 +0000 (09:43 +0000)]
migrated patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@434
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martinahansen [Wed, 27 May 2009 05:50:25 +0000 (05:50 +0000)]
migrated oligo_freq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@432
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martinahansen [Wed, 27 May 2009 05:34:40 +0000 (05:34 +0000)]
migrated trans family
git-svn-id: http://biopieces.googlecode.com/svn/trunk@430
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martinahansen [Wed, 27 May 2009 05:02:25 +0000 (05:02 +0000)]
migrated merge_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@427
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martinahansen [Wed, 27 May 2009 04:36:19 +0000 (04:36 +0000)]
migrated max, min, mean, and median _vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@426
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martinahansen [Wed, 27 May 2009 04:06:42 +0000 (04:06 +0000)]
migrated match_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@423
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martinahansen [Wed, 27 May 2009 03:52:20 +0000 (03:52 +0000)]
added 3 more
git-svn-id: http://biopieces.googlecode.com/svn/trunk@421
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martinahansen [Tue, 26 May 2009 17:41:50 +0000 (17:41 +0000)]
migrated 3 biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@419
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martinahansen [Tue, 26 May 2009 12:12:21 +0000 (12:12 +0000)]
migrated create_vmatch_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@417
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martinahansen [Tue, 26 May 2009 11:26:04 +0000 (11:26 +0000)]
migrated create_weight_matrix
git-svn-id: http://biopieces.googlecode.com/svn/trunk@416
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martinahansen [Tue, 26 May 2009 11:18:29 +0000 (11:18 +0000)]
migrated count_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@413
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martinahansen [Tue, 26 May 2009 10:57:23 +0000 (10:57 +0000)]
migrated count_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@412
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martinahansen [Tue, 26 May 2009 09:14:05 +0000 (09:14 +0000)]
migrated and fixed calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@410
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martinahansen [Mon, 25 May 2009 12:22:22 +0000 (12:22 +0000)]
migrated calc_bit_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@408
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martinahansen [Mon, 25 May 2009 07:40:26 +0000 (07:40 +0000)]
migrated blat_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@406
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martinahansen [Sun, 24 May 2009 20:45:58 +0000 (20:45 +0000)]
migrated assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@403
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martinahansen [Sun, 24 May 2009 19:49:12 +0000 (19:49 +0000)]
migrated split biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@401
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martinahansen [Sun, 24 May 2009 19:49:00 +0000 (19:49 +0000)]
migrated split biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@400
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martinahansen [Sun, 24 May 2009 19:23:10 +0000 (19:23 +0000)]
migrated random_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@398
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martinahansen [Sun, 24 May 2009 15:48:16 +0000 (15:48 +0000)]
magrated analyze biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@396
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martinahansen [Sun, 24 May 2009 15:48:07 +0000 (15:48 +0000)]
magrated analyze biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@395
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martinahansen [Sun, 24 May 2009 10:35:56 +0000 (10:35 +0000)]
migrated write_align
git-svn-id: http://biopieces.googlecode.com/svn/trunk@394
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martinahansen [Sun, 24 May 2009 10:08:01 +0000 (10:08 +0000)]
migrated align_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@391
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martinahansen [Sun, 24 May 2009 09:56:12 +0000 (09:56 +0000)]
migrated add_ident
git-svn-id: http://biopieces.googlecode.com/svn/trunk@390
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martinahansen [Sun, 24 May 2009 09:21:16 +0000 (09:21 +0000)]
migrated shuffle_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@387
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martinahansen [Sun, 24 May 2009 09:10:21 +0000 (09:10 +0000)]
migrated complement_seq and reverse_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@385
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martinahansen [Sat, 23 May 2009 20:51:25 +0000 (20:51 +0000)]
migrated extract_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@383
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martinahansen [Sat, 23 May 2009 19:51:55 +0000 (19:51 +0000)]
rewrite begin
git-svn-id: http://biopieces.googlecode.com/svn/trunk@381
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martinahansen [Thu, 14 May 2009 11:38:43 +0000 (11:38 +0000)]
polishing split_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@380
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martinahansen [Wed, 13 May 2009 15:33:17 +0000 (15:33 +0000)]
added lowercase_seq symlink
git-svn-id: http://biopieces.googlecode.com/svn/trunk@378
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martinahansen [Wed, 13 May 2009 15:32:09 +0000 (15:32 +0000)]
fixing lowercase_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@377
74ccb610-7750-0410-82ae-
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martinahansen [Wed, 13 May 2009 15:28:16 +0000 (15:28 +0000)]
fixed symlink trouble
git-svn-id: http://biopieces.googlecode.com/svn/trunk@376
74ccb610-7750-0410-82ae-
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martinahansen [Wed, 13 May 2009 15:20:09 +0000 (15:20 +0000)]
git-svn-id: http://biopieces.googlecode.com/svn/trunk@375
74ccb610-7750-0410-82ae-
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martinahansen [Wed, 13 May 2009 15:17:00 +0000 (15:17 +0000)]
git-svn-id: http://biopieces.googlecode.com/svn/trunk@374
74ccb610-7750-0410-82ae-
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martinahansen [Wed, 13 May 2009 07:39:58 +0000 (07:39 +0000)]
moved all binaries and created symlinks instead
git-svn-id: http://biopieces.googlecode.com/svn/trunk@373
74ccb610-7750-0410-82ae-
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martinahansen [Tue, 12 May 2009 20:37:35 +0000 (20:37 +0000)]
split Biopieces.pm into BioRun.pm and Biopieces.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@370
74ccb610-7750-0410-82ae-
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martinahansen [Tue, 12 May 2009 15:44:25 +0000 (15:44 +0000)]
changed wiki renderer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@369
74ccb610-7750-0410-82ae-
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