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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Fri, 5 Mar 2010 11:10:55 +0000 (11:10 +0000)]
wiggle tracks display - almost there
git-svn-id: http://biopieces.googlecode.com/svn/trunk@894
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martinahansen [Fri, 5 Mar 2010 10:22:45 +0000 (10:22 +0000)]
fixing wiggle tracks in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@893
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martinahansen [Thu, 4 Mar 2010 19:56:03 +0000 (19:56 +0000)]
reworked list_inflate/deflate
git-svn-id: http://biopieces.googlecode.com/svn/trunk@892
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martinahansen [Thu, 4 Mar 2010 10:08:56 +0000 (10:08 +0000)]
chasing wiggle bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@891
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martinahansen [Wed, 3 Mar 2010 12:31:51 +0000 (12:31 +0000)]
fixed bug in list_deflate
git-svn-id: http://biopieces.googlecode.com/svn/trunk@890
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martinahansen [Wed, 3 Mar 2010 10:18:46 +0000 (10:18 +0000)]
fixed empty Q_ID val in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@888
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martinahansen [Wed, 3 Mar 2010 07:57:08 +0000 (07:57 +0000)]
added find_gaps
git-svn-id: http://biopieces.googlecode.com/svn/trunk@887
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martinahansen [Tue, 2 Mar 2010 19:09:11 +0000 (19:09 +0000)]
fixed bug in Seq.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@886
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martinahansen [Tue, 2 Mar 2010 17:18:46 +0000 (17:18 +0000)]
cleaned up BGB track code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@885
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martinahansen [Tue, 2 Mar 2010 16:44:56 +0000 (16:44 +0000)]
merged BGB::Common.pm to BGB::Track.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@884
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martinahansen [Tue, 2 Mar 2010 11:55:31 +0000 (11:55 +0000)]
BGB cleanup of index.cgi
git-svn-id: http://biopieces.googlecode.com/svn/trunk@882
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martinahansen [Tue, 2 Mar 2010 11:35:32 +0000 (11:35 +0000)]
BGB cleanup of hrefs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@881
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martinahansen [Mon, 1 Mar 2010 14:58:51 +0000 (14:58 +0000)]
added center navigation to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@880
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martinahansen [Mon, 1 Mar 2010 11:30:33 +0000 (11:30 +0000)]
added wiggle to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@879
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martinahansen [Mon, 1 Mar 2010 11:27:28 +0000 (11:27 +0000)]
added wiggle to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@878
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martinahansen [Thu, 11 Feb 2010 16:51:56 +0000 (16:51 +0000)]
fixed issue in KISS.pm but more found
git-svn-id: http://biopieces.googlecode.com/svn/trunk@876
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martinahansen [Thu, 11 Feb 2010 16:35:57 +0000 (16:35 +0000)]
added option for database search to blat_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@875
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martinahansen [Wed, 10 Feb 2010 15:54:39 +0000 (15:54 +0000)]
fixed feature width issue
git-svn-id: http://biopieces.googlecode.com/svn/trunk@873
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martinahansen [Wed, 10 Feb 2010 15:24:49 +0000 (15:24 +0000)]
added arrows to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@872
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martinahansen [Tue, 9 Feb 2010 17:29:06 +0000 (17:29 +0000)]
added color routine to Draw.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@871
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martinahansen [Tue, 9 Feb 2010 16:19:48 +0000 (16:19 +0000)]
moving back to binned index and using JSON for storing
git-svn-id: http://biopieces.googlecode.com/svn/trunk@870
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martinahansen [Tue, 9 Feb 2010 14:04:16 +0000 (14:04 +0000)]
changed kiss score to bit_score instead of eval
git-svn-id: http://biopieces.googlecode.com/svn/trunk@869
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martinahansen [Sat, 6 Feb 2010 18:07:30 +0000 (18:07 +0000)]
added search function to NClist.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@867
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martinahansen [Sat, 6 Feb 2010 18:06:21 +0000 (18:06 +0000)]
fixed BGB search function
git-svn-id: http://biopieces.googlecode.com/svn/trunk@866
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martinahansen [Sat, 6 Feb 2010 17:50:02 +0000 (17:50 +0000)]
debugging search function in NClists.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@865
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martinahansen [Sat, 6 Feb 2010 17:35:31 +0000 (17:35 +0000)]
added search function to NClist.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@864
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martinahansen [Sat, 6 Feb 2010 16:17:10 +0000 (16:17 +0000)]
removed dir check from create_bowtie_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@863
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martinahansen [Sat, 6 Feb 2010 16:15:30 +0000 (16:15 +0000)]
shifted to NC list in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@862
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martinahansen [Sat, 6 Feb 2010 11:35:39 +0000 (11:35 +0000)]
added uniq_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@859
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martinahansen [Sat, 6 Feb 2010 11:34:35 +0000 (11:34 +0000)]
fix of read_kiss code comments
git-svn-id: http://biopieces.googlecode.com/svn/trunk@858
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martinahansen [Fri, 5 Feb 2010 12:55:30 +0000 (12:55 +0000)]
fixed bugs in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@857
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martinahansen [Wed, 3 Feb 2010 12:36:54 +0000 (12:36 +0000)]
added NClist.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@856
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martinahansen [Sun, 31 Jan 2010 10:07:15 +0000 (10:07 +0000)]
fixed sequence type guessing in create_blast_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@855
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martinahansen [Fri, 29 Jan 2010 09:17:30 +0000 (09:17 +0000)]
changed sorting in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@854
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martinahansen [Thu, 28 Jan 2010 08:35:50 +0000 (08:35 +0000)]
repair on plot_karyogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@852
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martinahansen [Thu, 28 Jan 2010 07:56:21 +0000 (07:56 +0000)]
repair on plot_karyogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@851
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martinahansen [Tue, 26 Jan 2010 16:07:06 +0000 (16:07 +0000)]
fixed a number of issues - grave bug in complement_seq!
git-svn-id: http://biopieces.googlecode.com/svn/trunk@850
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martinahansen [Mon, 25 Jan 2010 20:50:44 +0000 (20:50 +0000)]
add q_id specificity to assemblo_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@848
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martinahansen [Mon, 25 Jan 2010 20:14:05 +0000 (20:14 +0000)]
added strand specificity fo assemble_contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@847
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martinahansen [Sun, 24 Jan 2010 16:54:44 +0000 (16:54 +0000)]
cleanup BGB stuff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@845
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martinahansen [Fri, 22 Jan 2010 10:11:09 +0000 (10:11 +0000)]
fixed URI::Escape on q_id in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@843
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martinahansen [Thu, 21 Jan 2010 09:11:56 +0000 (09:11 +0000)]
added plot_lines
git-svn-id: http://biopieces.googlecode.com/svn/trunk@839
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martinahansen [Tue, 19 Jan 2010 08:45:44 +0000 (08:45 +0000)]
changed uclust engine from CD-hit to uclust
git-svn-id: http://biopieces.googlecode.com/svn/trunk@837
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martinahansen [Tue, 19 Jan 2010 08:16:09 +0000 (08:16 +0000)]
fixed strand bug in SAM.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@836
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martinahansen [Wed, 13 Jan 2010 15:03:26 +0000 (15:03 +0000)]
changed engine in cluster_seq to uclust
git-svn-id: http://biopieces.googlecode.com/svn/trunk@834
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martinahansen [Tue, 12 Jan 2010 09:09:54 +0000 (09:09 +0000)]
added cluster_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@833
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martinahansen [Tue, 5 Jan 2010 18:57:08 +0000 (18:57 +0000)]
cleanup of BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@830
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martinahansen [Fri, 25 Dec 2009 10:13:41 +0000 (10:13 +0000)]
added BGB_delete_track
git-svn-id: http://biopieces.googlecode.com/svn/trunk@828
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martinahansen [Thu, 17 Dec 2009 17:40:07 +0000 (17:40 +0000)]
added BGB_read_track
git-svn-id: http://biopieces.googlecode.com/svn/trunk@826
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martinahansen [Thu, 17 Dec 2009 13:56:25 +0000 (13:56 +0000)]
simplified BGB index scheme
git-svn-id: http://biopieces.googlecode.com/svn/trunk@825
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martinahansen [Wed, 16 Dec 2009 13:31:38 +0000 (13:31 +0000)]
todo fixes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@824
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martinahansen [Wed, 16 Dec 2009 12:20:05 +0000 (12:20 +0000)]
fixed bug in grab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@823
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martinahansen [Tue, 15 Dec 2009 16:30:37 +0000 (16:30 +0000)]
BGB cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@822
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martinahansen [Tue, 15 Dec 2009 16:10:41 +0000 (16:10 +0000)]
fixed bug in list_biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@821
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martinahansen [Tue, 15 Dec 2009 16:06:20 +0000 (16:06 +0000)]
BGB cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@820
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martinahansen [Tue, 15 Dec 2009 15:23:05 +0000 (15:23 +0000)]
added permalink to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@819
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martinahansen [Tue, 15 Dec 2009 13:07:27 +0000 (13:07 +0000)]
fixed BGB nav_start bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@818
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martinahansen [Tue, 15 Dec 2009 11:28:31 +0000 (11:28 +0000)]
added find_genes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@817
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martinahansen [Tue, 15 Dec 2009 11:15:39 +0000 (11:15 +0000)]
added track label to search function in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@815
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martinahansen [Tue, 15 Dec 2009 10:43:43 +0000 (10:43 +0000)]
fixed upload pipe
git-svn-id: http://biopieces.googlecode.com/svn/trunk@814
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martinahansen [Tue, 15 Dec 2009 08:07:20 +0000 (08:07 +0000)]
fixex index.cgi
git-svn-id: http://biopieces.googlecode.com/svn/trunk@813
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martinahansen [Tue, 15 Dec 2009 08:00:05 +0000 (08:00 +0000)]
this is the index we want from xeon
git-svn-id: http://biopieces.googlecode.com/svn/trunk@812
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martinahansen [Mon, 14 Dec 2009 15:29:37 +0000 (15:29 +0000)]
added BGB_intersect
git-svn-id: http://biopieces.googlecode.com/svn/trunk@810
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martinahansen [Mon, 14 Dec 2009 14:09:23 +0000 (14:09 +0000)]
renamed upload_to_bbrowser to BGB_upload
git-svn-id: http://biopieces.googlecode.com/svn/trunk@808
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martinahansen [Mon, 14 Dec 2009 13:56:40 +0000 (13:56 +0000)]
added BGB_list
git-svn-id: http://biopieces.googlecode.com/svn/trunk@806
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martinahansen [Mon, 14 Dec 2009 09:01:36 +0000 (09:01 +0000)]
renaming BBrowser to BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@805
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martinahansen [Mon, 14 Dec 2009 08:58:40 +0000 (08:58 +0000)]
replacing Bbrowser with BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@804
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martinahansen [Mon, 14 Dec 2009 08:28:45 +0000 (08:28 +0000)]
added kiss_intersect
git-svn-id: http://biopieces.googlecode.com/svn/trunk@803
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martinahansen [Fri, 11 Dec 2009 19:07:17 +0000 (19:07 +0000)]
fixed bug in translate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@802
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martinahansen [Thu, 10 Dec 2009 14:58:04 +0000 (14:58 +0000)]
fixed bug in uploader
git-svn-id: http://biopieces.googlecode.com/svn/trunk@801
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martinahansen [Thu, 10 Dec 2009 14:15:13 +0000 (14:15 +0000)]
fixed bug in upload_to_bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@800
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martinahansen [Tue, 8 Dec 2009 14:42:36 +0000 (14:42 +0000)]
added security to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@799
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martinahansen [Tue, 8 Dec 2009 14:21:21 +0000 (14:21 +0000)]
added read_ace
git-svn-id: http://biopieces.googlecode.com/svn/trunk@798
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martinahansen [Tue, 8 Dec 2009 13:26:55 +0000 (13:26 +0000)]
added login to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@796
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martinahansen [Fri, 4 Dec 2009 14:52:34 +0000 (14:52 +0000)]
added file_md5 routine to Filesys.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@795
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martinahansen [Thu, 3 Dec 2009 10:58:55 +0000 (10:58 +0000)]
added space between liniea track elements
git-svn-id: http://biopieces.googlecode.com/svn/trunk@794
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martinahansen [Thu, 3 Dec 2009 10:52:28 +0000 (10:52 +0000)]
fixed inline PNG in Bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@793
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martinahansen [Wed, 2 Dec 2009 12:08:13 +0000 (12:08 +0000)]
implemented search function in bbrowser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@792
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martinahansen [Tue, 1 Dec 2009 15:13:33 +0000 (15:13 +0000)]
added DB.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@791
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martinahansen [Tue, 1 Dec 2009 15:13:18 +0000 (15:13 +0000)]
added DB.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@790
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martinahansen [Tue, 1 Dec 2009 13:38:12 +0000 (13:38 +0000)]
set bbrowser and GFF to 0-base
git-svn-id: http://biopieces.googlecode.com/svn/trunk@789
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martinahansen [Tue, 1 Dec 2009 10:59:03 +0000 (10:59 +0000)]
fixed IO rename in write_kiss
git-svn-id: http://biopieces.googlecode.com/svn/trunk@787
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martinahansen [Tue, 1 Dec 2009 10:19:09 +0000 (10:19 +0000)]
rename mistake fix2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@786
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martinahansen [Tue, 1 Dec 2009 10:18:46 +0000 (10:18 +0000)]
rename mistake fix1
git-svn-id: http://biopieces.googlecode.com/svn/trunk@785
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martinahansen [Tue, 1 Dec 2009 10:17:08 +0000 (10:17 +0000)]
renamed KISS browser to Biopiece browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@784
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martinahansen [Fri, 27 Nov 2009 15:00:37 +0000 (15:00 +0000)]
added dna export to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@782
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martinahansen [Fri, 27 Nov 2009 09:46:06 +0000 (09:46 +0000)]
changes to browser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@781
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martinahansen [Thu, 26 Nov 2009 13:42:51 +0000 (13:42 +0000)]
cleaned BBrowser::Tracks.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@780
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martinahansen [Thu, 26 Nov 2009 12:57:52 +0000 (12:57 +0000)]
Cleaned BBrowser::Draw
git-svn-id: http://biopieces.googlecode.com/svn/trunk@779
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martinahansen [Thu, 26 Nov 2009 12:51:35 +0000 (12:51 +0000)]
cleaned KISS.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@778
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martinahansen [Thu, 26 Nov 2009 12:37:36 +0000 (12:37 +0000)]
finished cleaning index.cgi
git-svn-id: http://biopieces.googlecode.com/svn/trunk@777
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martinahansen [Thu, 26 Nov 2009 12:30:19 +0000 (12:30 +0000)]
removed KISS directory
git-svn-id: http://biopieces.googlecode.com/svn/trunk@776
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martinahansen [Thu, 26 Nov 2009 11:38:50 +0000 (11:38 +0000)]
www relayout
git-svn-id: http://biopieces.googlecode.com/svn/trunk@775
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 26 Nov 2009 11:37:47 +0000 (11:37 +0000)]
www relayout
git-svn-id: http://biopieces.googlecode.com/svn/trunk@774
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Wed, 25 Nov 2009 20:16:24 +0000 (20:16 +0000)]
more KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@773
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Wed, 25 Nov 2009 15:02:46 +0000 (15:02 +0000)]
fixed color palette in KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@772
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Wed, 25 Nov 2009 13:40:29 +0000 (13:40 +0000)]
fixed KISS browser genome selection
git-svn-id: http://biopieces.googlecode.com/svn/trunk@771
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 24 Nov 2009 19:44:23 +0000 (19:44 +0000)]
fixed comma bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@770
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 24 Nov 2009 17:26:35 +0000 (17:26 +0000)]
kiss_sort()
git-svn-id: http://biopieces.googlecode.com/svn/trunk@769
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 24 Nov 2009 17:20:50 +0000 (17:20 +0000)]
fixed KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@768
74ccb610-7750-0410-82ae-
013aeee3265d
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