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git.donarmstrong.com Git - biopieces.git/log
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
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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
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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
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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
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martinahansen [Thu, 4 Sep 2008 23:46:14 +0000 (23:46 +0000)]
bipartite_scan.c alpha
git-svn-id: http://biopieces.googlecode.com/svn/trunk@244
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martinahansen [Wed, 3 Sep 2008 07:43:45 +0000 (07:43 +0000)]
removed wiggle options from upload_to_ucsc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@243
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martinahansen [Wed, 3 Sep 2008 05:46:38 +0000 (05:46 +0000)]
fixed -S and -L for calc_fixedstep biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@241
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martinahansen [Wed, 3 Sep 2008 05:26:07 +0000 (05:26 +0000)]
added calc_fixedstep biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@240
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martinahansen [Mon, 1 Sep 2008 01:27:36 +0000 (01:27 +0000)]
read_solexa now handles both decimal and octal scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@235
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martinahansen [Fri, 29 Aug 2008 07:36:32 +0000 (07:36 +0000)]
fixed bug in remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@234
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martinahansen [Fri, 29 Aug 2008 07:04:00 +0000 (07:04 +0000)]
fixed minor bugs in remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@232
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martinahansen [Fri, 29 Aug 2008 06:51:02 +0000 (06:51 +0000)]
added remove_adaptor biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@231
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martinahansen [Fri, 29 Aug 2008 06:49:49 +0000 (06:49 +0000)]
added remove_adaptor biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@230
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martinahansen [Fri, 29 Aug 2008 00:50:16 +0000 (00:50 +0000)]
fixed UCSC::get_psl_entry
git-svn-id: http://biopieces.googlecode.com/svn/trunk@229
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martinahansen [Thu, 28 Aug 2008 05:22:35 +0000 (05:22 +0000)]
fix of \r feature in Fasta::get_entry
git-svn-id: http://biopieces.googlecode.com/svn/trunk@228
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martinahansen [Thu, 28 Aug 2008 05:12:19 +0000 (05:12 +0000)]
read_fasta fix for stupid \r
git-svn-id: http://biopieces.googlecode.com/svn/trunk@227
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martinahansen [Tue, 26 Aug 2008 03:49:54 +0000 (03:49 +0000)]
fixed bug in table name check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@226
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martinahansen [Tue, 26 Aug 2008 01:55:37 +0000 (01:55 +0000)]
made speedup for repeat-O-matic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@225
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martinahansen [Tue, 26 Aug 2008 01:36:32 +0000 (01:36 +0000)]
added fixedStep format to upload_to_ucsc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@224
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martinahansen [Mon, 25 Aug 2008 07:59:34 +0000 (07:59 +0000)]
clean-write of repeat-O-matic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@222
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martinahansen [Mon, 25 Aug 2008 05:48:07 +0000 (05:48 +0000)]
added --verbose run option for blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@221
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martinahansen [Mon, 25 Aug 2008 00:20:17 +0000 (00:20 +0000)]
added revcomp_dna to repeat-O-matic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@220
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martinahansen [Fri, 22 Aug 2008 04:47:44 +0000 (04:47 +0000)]
fixed read_soft to deal with stupid Soft format feature
git-svn-id: http://biopieces.googlecode.com/svn/trunk@219
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martinahansen [Fri, 22 Aug 2008 01:33:23 +0000 (01:33 +0000)]
added option to read_soft for selecting specific samples
git-svn-id: http://biopieces.googlecode.com/svn/trunk@218
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martinahansen [Thu, 21 Aug 2008 07:57:55 +0000 (07:57 +0000)]
finished c fasta parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@217
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martinahansen [Thu, 21 Aug 2008 07:50:28 +0000 (07:50 +0000)]
finished c fasta parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@216
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martinahansen [Thu, 21 Aug 2008 04:01:58 +0000 (04:01 +0000)]
fixed format_genome
git-svn-id: http://biopieces.googlecode.com/svn/trunk@215
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martinahansen [Thu, 21 Aug 2008 03:55:34 +0000 (03:55 +0000)]
fixed bug in vmatch_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@214
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martinahansen [Thu, 21 Aug 2008 00:28:06 +0000 (00:28 +0000)]
fixed %d->%f for log10 in upload_to_ucsc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@213
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martinahansen [Thu, 21 Aug 2008 00:27:09 +0000 (00:27 +0000)]
more updates of c and fixes to upload_to_ucsc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@212
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martinahansen [Mon, 18 Aug 2008 09:02:40 +0000 (09:02 +0000)]
another c code upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@210
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martinahansen [Thu, 14 Aug 2008 08:35:21 +0000 (08:35 +0000)]
updated read_solexa
git-svn-id: http://biopieces.googlecode.com/svn/trunk@208
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martinahansen [Thu, 14 Aug 2008 06:03:44 +0000 (06:03 +0000)]
unit test of mem.c done
git-svn-id: http://biopieces.googlecode.com/svn/trunk@207
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martinahansen [Wed, 13 Aug 2008 23:35:20 +0000 (23:35 +0000)]
update of c libs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@206
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martinahansen [Tue, 5 Aug 2008 00:22:07 +0000 (00:22 +0000)]
fixing up c code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@203
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martinahansen [Fri, 1 Aug 2008 04:56:16 +0000 (04:56 +0000)]
changed result key of count_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@202
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martinahansen [Tue, 29 Jul 2008 07:45:46 +0000 (07:45 +0000)]
reverted code for format_genome in order to make vmatch_seq work correctly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@200
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martinahansen [Tue, 29 Jul 2008 07:07:46 +0000 (07:07 +0000)]
correcting bug in Match.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@199
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martinahansen [Tue, 29 Jul 2008 02:21:10 +0000 (02:21 +0000)]
finished biopiece merge_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@198
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martinahansen [Mon, 28 Jul 2008 12:23:23 +0000 (12:23 +0000)]
added new biopiece merge_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@197
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martinahansen [Fri, 25 Jul 2008 05:00:01 +0000 (05:00 +0000)]
fixed zero entry tmp file bug in soap_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@196
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martinahansen [Fri, 25 Jul 2008 04:21:03 +0000 (04:21 +0000)]
fixed another annoying bug in clean_tmp()
git-svn-id: http://biopieces.googlecode.com/svn/trunk@195
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martinahansen [Fri, 25 Jul 2008 03:06:16 +0000 (03:06 +0000)]
corrected bug in clean tmp to deal with permision problem
git-svn-id: http://biopieces.googlecode.com/svn/trunk@194
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martinahansen [Fri, 25 Jul 2008 01:12:54 +0000 (01:12 +0000)]
changed error output to fit on screen
git-svn-id: http://biopieces.googlecode.com/svn/trunk@193
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martinahansen [Thu, 24 Jul 2008 07:49:26 +0000 (07:49 +0000)]
added seed_size to soap_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@192
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martinahansen [Thu, 24 Jul 2008 06:42:45 +0000 (06:42 +0000)]
corrected ugly bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@190
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martinahansen [Thu, 24 Jul 2008 06:27:53 +0000 (06:27 +0000)]
fixed cleanup of temporary files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@189
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martinahansen [Wed, 23 Jul 2008 02:11:07 +0000 (02:11 +0000)]
begin of status update
git-svn-id: http://biopieces.googlecode.com/svn/trunk@188
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martinahansen [Tue, 22 Jul 2008 01:25:07 +0000 (01:25 +0000)]
added record2fasta to allow for aliasing of SEQ_NAME to Q_ID or S_ID
git-svn-id: http://biopieces.googlecode.com/svn/trunk@187
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martinahansen [Mon, 21 Jul 2008 23:42:56 +0000 (23:42 +0000)]
updated upload_to_ucsc wiki and added a secure free to c code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@186
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martinahansen [Mon, 21 Jul 2008 06:58:01 +0000 (06:58 +0000)]
fixed ugly bug in get_record
git-svn-id: http://biopieces.googlecode.com/svn/trunk@184
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martinahansen [Mon, 21 Jul 2008 06:31:00 +0000 (06:31 +0000)]
corrected an ugly bug in get_record
git-svn-id: http://biopieces.googlecode.com/svn/trunk@183
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