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biopieces.git
15 years agodoc update
martinahansen [Tue, 18 Nov 2008 04:01:34 +0000 (04:01 +0000)]
doc update

git-svn-id: http://biopieces.googlecode.com/svn/trunk@317 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoclean up
martinahansen [Tue, 18 Nov 2008 03:59:51 +0000 (03:59 +0000)]
clean up

git-svn-id: http://biopieces.googlecode.com/svn/trunk@316 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded -c switch to write_bed
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded ucscMakeTracks -b run to remove_ucsc_tracks
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofinished remove_ucsc_tracks
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofix date and time in ucsc config
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded remove_ucsc_tracks
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded -t to remove_mysql_tables
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoswapped bedSort with bed_sort
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded mysql related Biopieces
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofinished assemble_tag_contigs
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agorewrote grab to get speed
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed compute
martinahansen [Tue, 28 Oct 2008 07:31:47 +0000 (07:31 +0000)]
fixed compute

git-svn-id: http://biopieces.googlecode.com/svn/trunk@281 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed bug in compute and analyze_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agochanged delimiter in REC_TYPE SOLID to ;
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded REC_TYPE to read_solid
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoempty change to Seq.pm
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agotada
martinahansen [Mon, 29 Sep 2008 03:34:22 +0000 (03:34 +0000)]
tada

git-svn-id: http://biopieces.googlecode.com/svn/trunk@272 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed ugly bug
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed rename bug
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadding rescan to bipartite_scan
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed STDERR and verbose
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadd bipartite_decode
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadd bipartite_decode
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agobackup time
martinahansen [Tue, 23 Sep 2008 05:09:10 +0000 (05:09 +0000)]
backup time

git-svn-id: http://biopieces.googlecode.com/svn/trunk@263 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded SPAN to read_psl
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed tmp dir cleaner in Biopieces.pm
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded 5prime adaptor feature to remove_adaptor
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoinline::c code for adaptor removal
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agominor updates
martinahansen [Tue, 16 Sep 2008 00:06:05 +0000 (00:06 +0000)]
minor updates

git-svn-id: http://biopieces.googlecode.com/svn/trunk@257 74ccb610-7750-0410-82ae-013aeee3265d

15 years agobed_sort created
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded bed stuff to c code
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded copyright to c stuff
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agobipartite_scan polish2
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agolinked list sort added
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agobipartite_scan polish
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed 0 offset bug in remove_adaptor
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-013aeee3265d

15 years agoadded sort to bipartite_scan.c
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-013aeee3265d

15 years agobipartite_scan now working
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded c temp file dir
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-013aeee3265d

15 years agoadded unit test to mem.c
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-013aeee3265d

15 years agobipartite_scan.c alpha
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoremoved wiggle options from upload_to_ucsc
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed -S and -L for calc_fixedstep biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded calc_fixedstep biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoread_solexa now handles both decimal and octal scores
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed bug in remove_adaptor
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed minor bugs in remove_adaptor
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded remove_adaptor biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded remove_adaptor biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed UCSC::get_psl_entry
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofix of \r feature in Fasta::get_entry
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoread_fasta fix for stupid \r
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed bug in table name check
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agomade speedup for repeat-O-matic
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded fixedStep format to upload_to_ucsc
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoclean-write of repeat-O-matic
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded --verbose run option for blast_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded revcomp_dna to repeat-O-matic
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed read_soft to deal with stupid Soft format feature
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded option to read_soft for selecting specific samples
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofinished c fasta parser
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofinished c fasta parser
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed format_genome
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed bug in vmatch_index
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed %d->%f for log10 in upload_to_ucsc
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agomore updates of c and fixes to upload_to_ucsc
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoanother c code upgrade
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoupdated read_solexa
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agounit test of mem.c done
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoupdate of c libs
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixing up c code
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agochanged result key of count_records
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoreverted code for format_genome in order to make vmatch_seq work correctly
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agocorrecting bug in Match.pm
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofinished biopiece merge_records
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded new biopiece merge_records
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed zero entry tmp file bug in soap_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed another annoying bug in clean_tmp()
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agocorrected bug in clean tmp to deal with permision problem
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agochanged error output to fit on screen
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded seed_size to soap_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agocorrected ugly bug
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed cleanup of temporary files
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agobegin of status update
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded record2fasta to allow for aliasing of SEQ_NAME to Q_ID or S_ID
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoupdated upload_to_ucsc wiki and added a secure free to c code
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed ugly bug in get_record
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agocorrected an ugly bug in get_record
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 74ccb610-7750-0410-82ae-013aeee3265d

15 years agomore soap_seq debugging
martinahansen [Mon, 21 Jul 2008 05:57:41 +0000 (05:57 +0000)]
more soap_seq debugging

git-svn-id: http://biopieces.googlecode.com/svn/trunk@182 74ccb610-7750-0410-82ae-013aeee3265d

15 years agodebugging soap_seq
martinahansen [Mon, 21 Jul 2008 05:46:27 +0000 (05:46 +0000)]
debugging soap_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@181 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded soap_seq
martinahansen [Mon, 21 Jul 2008 05:17:55 +0000 (05:17 +0000)]
added soap_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@180 74ccb610-7750-0410-82ae-013aeee3265d

15 years agochanged wib dir from BP_DATA to ~/ucsc
martinahansen [Mon, 21 Jul 2008 03:50:48 +0000 (03:50 +0000)]
changed wib dir from BP_DATA to ~/ucsc

git-svn-id: http://biopieces.googlecode.com/svn/trunk@178 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoupdated list_genomes wiki and bashrc
martinahansen [Mon, 21 Jul 2008 01:08:14 +0000 (01:08 +0000)]
updated list_genomes wiki and bashrc

git-svn-id: http://biopieces.googlecode.com/svn/trunk@177 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixed local and global logging
martinahansen [Mon, 21 Jul 2008 00:15:36 +0000 (00:15 +0000)]
fixed local and global logging

git-svn-id: http://biopieces.googlecode.com/svn/trunk@174 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoadded a variable argument list example to c scr
martinahansen [Sun, 20 Jul 2008 23:50:53 +0000 (23:50 +0000)]
added a variable argument list example to c scr

git-svn-id: http://biopieces.googlecode.com/svn/trunk@173 74ccb610-7750-0410-82ae-013aeee3265d

15 years agocleaning c source dir
martinahansen [Sun, 20 Jul 2008 01:11:58 +0000 (01:11 +0000)]
cleaning c source dir

git-svn-id: http://biopieces.googlecode.com/svn/trunk@172 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixing bashrc
martinahansen [Thu, 17 Jul 2008 04:21:05 +0000 (04:21 +0000)]
fixing bashrc

git-svn-id: http://biopieces.googlecode.com/svn/trunk@170 74ccb610-7750-0410-82ae-013aeee3265d

15 years agofixing bashrc
martinahansen [Thu, 17 Jul 2008 04:20:43 +0000 (04:20 +0000)]
fixing bashrc

git-svn-id: http://biopieces.googlecode.com/svn/trunk@169 74ccb610-7750-0410-82ae-013aeee3265d

15 years agoremoved bp_usage dir from source trunk (should be root of wiki trunk)
martinahansen [Thu, 17 Jul 2008 04:11:13 +0000 (04:11 +0000)]
removed bp_usage dir from source trunk (should be root of wiki trunk)

git-svn-id: http://biopieces.googlecode.com/svn/trunk@168 74ccb610-7750-0410-82ae-013aeee3265d