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git.donarmstrong.com Git - biopieces.git/log
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
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martinahansen [Thu, 26 Nov 2009 11:37:47 +0000 (11:37 +0000)]
www relayout
git-svn-id: http://biopieces.googlecode.com/svn/trunk@774
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martinahansen [Wed, 25 Nov 2009 20:16:24 +0000 (20:16 +0000)]
more KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@773
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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
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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
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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
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martinahansen [Tue, 24 Nov 2009 17:26:35 +0000 (17:26 +0000)]
kiss_sort()
git-svn-id: http://biopieces.googlecode.com/svn/trunk@769
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martinahansen [Tue, 24 Nov 2009 17:20:50 +0000 (17:20 +0000)]
fixed KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@768
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martinahansen [Tue, 24 Nov 2009 13:11:00 +0000 (13:11 +0000)]
rewrote upload_to_KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@767
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martinahansen [Tue, 24 Nov 2009 11:19:17 +0000 (11:19 +0000)]
major work on KISS browser completed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@766
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martinahansen [Mon, 16 Nov 2009 10:47:11 +0000 (10:47 +0000)]
hacked read_soft to deal with soft_files wo platform table
git-svn-id: http://biopieces.googlecode.com/svn/trunk@762
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martinahansen [Mon, 16 Nov 2009 07:39:44 +0000 (07:39 +0000)]
misc changes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@760
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martinahansen [Fri, 13 Nov 2009 10:03:31 +0000 (10:03 +0000)]
write_kiss now do blast output
git-svn-id: http://biopieces.googlecode.com/svn/trunk@759
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martinahansen [Mon, 9 Nov 2009 14:15:46 +0000 (14:15 +0000)]
added analyze_snp
git-svn-id: http://biopieces.googlecode.com/svn/trunk@758
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martinahansen [Mon, 9 Nov 2009 12:26:57 +0000 (12:26 +0000)]
fixed SAM bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@756
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martinahansen [Mon, 9 Nov 2009 08:43:40 +0000 (08:43 +0000)]
improved SAM parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@752
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martinahansen [Thu, 5 Nov 2009 13:02:13 +0000 (13:02 +0000)]
fixed KISS align code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@748
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martinahansen [Wed, 4 Nov 2009 20:07:13 +0000 (20:07 +0000)]
corrected ALIGN implementation
git-svn-id: http://biopieces.googlecode.com/svn/trunk@747
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martinahansen [Wed, 4 Nov 2009 08:06:24 +0000 (08:06 +0000)]
fixed details in bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@743
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martinahansen [Fri, 30 Oct 2009 10:55:41 +0000 (10:55 +0000)]
added read_sam
git-svn-id: http://biopieces.googlecode.com/svn/trunk@724
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martinahansen [Thu, 29 Oct 2009 15:10:11 +0000 (15:10 +0000)]
fixed bug in patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@721
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martinahansen [Thu, 29 Oct 2009 13:52:45 +0000 (13:52 +0000)]
modified split_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@718
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martinahansen [Thu, 29 Oct 2009 10:46:50 +0000 (10:46 +0000)]
corrected error message in dir_create
git-svn-id: http://biopieces.googlecode.com/svn/trunk@715
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martinahansen [Wed, 28 Oct 2009 17:19:29 +0000 (17:19 +0000)]
KISS browser working, but slow
git-svn-id: http://biopieces.googlecode.com/svn/trunk@714
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martinahansen [Wed, 28 Oct 2009 09:30:09 +0000 (09:30 +0000)]
added ALIGN view support to KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@713
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martinahansen [Tue, 27 Oct 2009 17:02:09 +0000 (17:02 +0000)]
more work on KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@712
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martinahansen [Tue, 27 Oct 2009 07:47:58 +0000 (07:47 +0000)]
revised KISS format
git-svn-id: http://biopieces.googlecode.com/svn/trunk@710
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martinahansen [Sat, 24 Oct 2009 20:26:48 +0000 (20:26 +0000)]
added zoom and move to KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@709
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martinahansen [Fri, 23 Oct 2009 08:11:35 +0000 (08:11 +0000)]
removed jbrowse support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@708
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martinahansen [Thu, 22 Oct 2009 07:10:50 +0000 (07:10 +0000)]
KISS upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@707
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martinahansen [Thu, 22 Oct 2009 05:48:35 +0000 (05:48 +0000)]
added www
git-svn-id: http://biopieces.googlecode.com/svn/trunk@706
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martinahansen [Wed, 21 Oct 2009 19:03:54 +0000 (19:03 +0000)]
changed KISS format
git-svn-id: http://biopieces.googlecode.com/svn/trunk@705
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martinahansen [Wed, 21 Oct 2009 16:43:09 +0000 (16:43 +0000)]
added upload_to_KISS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@703
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martinahansen [Wed, 21 Oct 2009 14:34:27 +0000 (14:34 +0000)]
added kiss biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@701
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martinahansen [Wed, 21 Oct 2009 06:04:03 +0000 (06:04 +0000)]
fixed dna/DNA bug in Align.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@699
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martinahansen [Mon, 19 Oct 2009 13:28:17 +0000 (13:28 +0000)]
added XHTML
git-svn-id: http://biopieces.googlecode.com/svn/trunk@698
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