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git.donarmstrong.com Git - biopieces.git/log
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
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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
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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
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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
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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
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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
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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
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martinahansen [Wed, 17 Dec 2008 23:53:33 +0000 (23:53 +0000)]
fixed BED BUG
git-svn-id: http://biopieces.googlecode.com/svn/trunk@357
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martinahansen [Thu, 11 Dec 2008 08:06:42 +0000 (08:06 +0000)]
lots of PSL related changes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@356
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martinahansen [Thu, 11 Dec 2008 05:05:17 +0000 (05:05 +0000)]
added exon capabilities to calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@355
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martinahansen [Thu, 11 Dec 2008 03:55:05 +0000 (03:55 +0000)]
calc_fixedstep reverted to perl
git-svn-id: http://biopieces.googlecode.com/svn/trunk@354
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martinahansen [Thu, 11 Dec 2008 00:54:44 +0000 (00:54 +0000)]
fixed carriage return bug in read_ucsc_config
git-svn-id: http://biopieces.googlecode.com/svn/trunk@353
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martinahansen [Tue, 9 Dec 2008 04:17:24 +0000 (04:17 +0000)]
added splice to get_genome_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@346
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martinahansen [Tue, 9 Dec 2008 04:05:58 +0000 (04:05 +0000)]
fixed bug in remove_ucsc_tracks
git-svn-id: http://biopieces.googlecode.com/svn/trunk@344
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martinahansen [Mon, 8 Dec 2008 05:55:36 +0000 (05:55 +0000)]
minor fixes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@342
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martinahansen [Mon, 8 Dec 2008 03:57:44 +0000 (03:57 +0000)]
added --check to a number of Biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@341
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martinahansen [Mon, 8 Dec 2008 02:44:01 +0000 (02:44 +0000)]
reverting to BED lists
git-svn-id: http://biopieces.googlecode.com/svn/trunk@339
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martinahansen [Mon, 8 Dec 2008 02:21:11 +0000 (02:21 +0000)]
changed BED.pm from list to hash
git-svn-id: http://biopieces.googlecode.com/svn/trunk@338
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martinahansen [Mon, 8 Dec 2008 00:32:14 +0000 (00:32 +0000)]
made check_bed optional
git-svn-id: http://biopieces.googlecode.com/svn/trunk@337
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martinahansen [Fri, 5 Dec 2008 06:02:53 +0000 (06:02 +0000)]
fixed CHR_BEG=0 bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@335
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martinahansen [Fri, 5 Dec 2008 05:25:24 +0000 (05:25 +0000)]
changed barray from ushort to uint
git-svn-id: http://biopieces.googlecode.com/svn/trunk@334
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martinahansen [Fri, 5 Dec 2008 05:16:39 +0000 (05:16 +0000)]
added bed2tag_contigs as backend to assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@333
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martinahansen [Fri, 5 Dec 2008 03:03:11 +0000 (03:03 +0000)]
added bed2tag_contigs.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@331
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martinahansen [Fri, 5 Dec 2008 02:52:08 +0000 (02:52 +0000)]
added bed2fixedstep.c as backend to calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@330
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martinahansen [Fri, 5 Dec 2008 01:14:50 +0000 (01:14 +0000)]
fixed bed2fixedstep.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@329
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martinahansen [Thu, 4 Dec 2008 10:18:04 +0000 (10:18 +0000)]
added python code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@328
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martinahansen [Thu, 4 Dec 2008 04:05:27 +0000 (04:05 +0000)]
added bed2fixedstep.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@327
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martinahansen [Sun, 30 Nov 2008 09:20:03 +0000 (09:20 +0000)]
added barray.c and cleaned hash.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@326
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martinahansen [Fri, 28 Nov 2008 01:07:10 +0000 (01:07 +0000)]
removed GIW2008 poster to docs and added to featured dls instead
git-svn-id: http://biopieces.googlecode.com/svn/trunk@325
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martinahansen [Fri, 28 Nov 2008 00:58:24 +0000 (00:58 +0000)]
added GIW2008 poster to docs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@324
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martinahansen [Thu, 27 Nov 2008 02:57:52 +0000 (02:57 +0000)]
added c power to calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@323
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martinahansen [Mon, 24 Nov 2008 02:27:44 +0000 (02:27 +0000)]
fixed bugs in calc_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@321
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martinahansen [Mon, 24 Nov 2008 00:33:54 +0000 (00:33 +0000)]
fixed bugs in assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@320
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martinahansen [Mon, 24 Nov 2008 00:13:00 +0000 (00:13 +0000)]
major code upgrade 1
git-svn-id: http://biopieces.googlecode.com/svn/trunk@319
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martinahansen [Fri, 21 Nov 2008 06:48:00 +0000 (06:48 +0000)]
fixed bug in compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@318
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martinahansen [Tue, 18 Nov 2008 04:01:34 +0000 (04:01 +0000)]
doc update
git-svn-id: http://biopieces.googlecode.com/svn/trunk@317
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martinahansen [Tue, 18 Nov 2008 03:59:51 +0000 (03:59 +0000)]
clean up
git-svn-id: http://biopieces.googlecode.com/svn/trunk@316
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martinahansen [Thu, 13 Nov 2008 01:22:00 +0000 (01:22 +0000)]
added -c switch to write_bed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@310
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martinahansen [Tue, 11 Nov 2008 10:16:03 +0000 (10:16 +0000)]
added ucscMakeTracks -b run to remove_ucsc_tracks
git-svn-id: http://biopieces.googlecode.com/svn/trunk@308
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martinahansen [Tue, 11 Nov 2008 07:03:12 +0000 (07:03 +0000)]
finished remove_ucsc_tracks
git-svn-id: http://biopieces.googlecode.com/svn/trunk@307
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martinahansen [Tue, 11 Nov 2008 06:37:05 +0000 (06:37 +0000)]
fix date and time in ucsc config
git-svn-id: http://biopieces.googlecode.com/svn/trunk@305
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martinahansen [Tue, 11 Nov 2008 06:26:04 +0000 (06:26 +0000)]
added remove_ucsc_tracks
git-svn-id: http://biopieces.googlecode.com/svn/trunk@304
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martinahansen [Tue, 11 Nov 2008 04:33:37 +0000 (04:33 +0000)]
added -t to remove_mysql_tables
git-svn-id: http://biopieces.googlecode.com/svn/trunk@302
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martinahansen [Tue, 11 Nov 2008 04:24:45 +0000 (04:24 +0000)]
swapped bedSort with bed_sort
git-svn-id: http://biopieces.googlecode.com/svn/trunk@301
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martinahansen [Tue, 11 Nov 2008 04:22:48 +0000 (04:22 +0000)]
added mysql related Biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@300
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martinahansen [Fri, 7 Nov 2008 10:42:23 +0000 (10:42 +0000)]
finished assemble_tag_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@297
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martinahansen [Mon, 3 Nov 2008 08:07:35 +0000 (08:07 +0000)]
rewrote grab to get speed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@292
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martinahansen [Tue, 28 Oct 2008 07:31:47 +0000 (07:31 +0000)]
fixed compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@281
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martinahansen [Tue, 28 Oct 2008 04:58:28 +0000 (04:58 +0000)]
fixed bug in compute and analyze_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@279
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martinahansen [Mon, 27 Oct 2008 02:44:50 +0000 (02:44 +0000)]
changed delimiter in REC_TYPE SOLID to ;
git-svn-id: http://biopieces.googlecode.com/svn/trunk@278
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martinahansen [Thu, 2 Oct 2008 03:47:43 +0000 (03:47 +0000)]
added REC_TYPE to read_solid
git-svn-id: http://biopieces.googlecode.com/svn/trunk@275
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martinahansen [Mon, 29 Sep 2008 03:36:40 +0000 (03:36 +0000)]
empty change to Seq.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@273
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martinahansen [Mon, 29 Sep 2008 03:34:22 +0000 (03:34 +0000)]
tada
git-svn-id: http://biopieces.googlecode.com/svn/trunk@272
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martinahansen [Thu, 25 Sep 2008 02:06:09 +0000 (02:06 +0000)]
fixed ugly bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@270
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martinahansen [Thu, 25 Sep 2008 01:34:06 +0000 (01:34 +0000)]
fixed rename bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@269
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martinahansen [Wed, 24 Sep 2008 04:34:12 +0000 (04:34 +0000)]
adding rescan to bipartite_scan
git-svn-id: http://biopieces.googlecode.com/svn/trunk@267
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martinahansen [Tue, 23 Sep 2008 06:45:50 +0000 (06:45 +0000)]
fixed STDERR and verbose
git-svn-id: http://biopieces.googlecode.com/svn/trunk@266
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martinahansen [Tue, 23 Sep 2008 06:41:33 +0000 (06:41 +0000)]
add bipartite_decode
git-svn-id: http://biopieces.googlecode.com/svn/trunk@265
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martinahansen [Tue, 23 Sep 2008 06:30:39 +0000 (06:30 +0000)]
add bipartite_decode
git-svn-id: http://biopieces.googlecode.com/svn/trunk@264
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martinahansen [Tue, 23 Sep 2008 05:09:10 +0000 (05:09 +0000)]
backup time
git-svn-id: http://biopieces.googlecode.com/svn/trunk@263
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martinahansen [Wed, 17 Sep 2008 23:50:37 +0000 (23:50 +0000)]
added SPAN to read_psl
git-svn-id: http://biopieces.googlecode.com/svn/trunk@262
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martinahansen [Wed, 17 Sep 2008 23:35:20 +0000 (23:35 +0000)]
fixed tmp dir cleaner in Biopieces.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@260
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martinahansen [Tue, 16 Sep 2008 08:43:02 +0000 (08:43 +0000)]
added 5prime adaptor feature to remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@259
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martinahansen [Tue, 16 Sep 2008 04:36:54 +0000 (04:36 +0000)]
inline::c code for adaptor removal
git-svn-id: http://biopieces.googlecode.com/svn/trunk@258
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martinahansen [Tue, 16 Sep 2008 00:06:05 +0000 (00:06 +0000)]
minor updates
git-svn-id: http://biopieces.googlecode.com/svn/trunk@257
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martinahansen [Thu, 11 Sep 2008 11:50:50 +0000 (11:50 +0000)]
bed_sort created
git-svn-id: http://biopieces.googlecode.com/svn/trunk@256
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martinahansen [Thu, 11 Sep 2008 09:09:20 +0000 (09:09 +0000)]
added bed stuff to c code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@255
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martinahansen [Wed, 10 Sep 2008 11:16:25 +0000 (11:16 +0000)]
added copyright to c stuff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@254
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martinahansen [Wed, 10 Sep 2008 06:52:46 +0000 (06:52 +0000)]
bipartite_scan polish2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@253
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martinahansen [Wed, 10 Sep 2008 06:48:48 +0000 (06:48 +0000)]
linked list sort added
git-svn-id: http://biopieces.googlecode.com/svn/trunk@252
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martinahansen [Wed, 10 Sep 2008 06:45:09 +0000 (06:45 +0000)]
bipartite_scan polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@251
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martinahansen [Mon, 8 Sep 2008 05:29:45 +0000 (05:29 +0000)]
fixed 0 offset bug in remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@250
74ccb610-7750-0410-82ae-
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martinahansen [Mon, 8 Sep 2008 01:50:55 +0000 (01:50 +0000)]
added sort to bipartite_scan.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@248
74ccb610-7750-0410-82ae-
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martinahansen [Fri, 5 Sep 2008 07:17:33 +0000 (07:17 +0000)]
bipartite_scan now working
git-svn-id: http://biopieces.googlecode.com/svn/trunk@247
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martinahansen [Fri, 5 Sep 2008 03:43:15 +0000 (03:43 +0000)]
added c temp file dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@246
74ccb610-7750-0410-82ae-
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martinahansen [Fri, 5 Sep 2008 03:13:04 +0000 (03:13 +0000)]
added unit test to mem.c
git-svn-id: http://biopieces.googlecode.com/svn/trunk@245
74ccb610-7750-0410-82ae-
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