 Peter Cock
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720dea16dc
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Fix for BLAST XML to tabular when both query and subject have XXX masking
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2011-05-18 18:43:46 +01:00 |
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Kanwei Li
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68a514d789
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Fix a few XSS issues in workflow/history
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2011-05-25 11:31:26 +02:00 |
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Nate Coraor
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5dbf59c2fc
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Fix the non-working default="true" for checkboxes, thanks Louise-Amélie Schmitt.
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2011-05-24 05:33:07 -04:00 |
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Jeremy Goecks
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6e807d0f09
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Enable tags and annotations to work for new datasets in history. Fixes #550
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2011-05-24 02:20:35 +02:00 |
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Jeremy Goecks
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fe60a1ea8b
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When adding tracks to Trackster, add them in the order that they appear in the dataset listing.
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2011-05-22 23:54:01 +02:00 |
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Greg Von Kuster
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212433fe2c
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First pass of the next-gen Galaxy tool shed. See it demonsrated and discussed at the 2011 Gallaxy Community Conference in Lunteren on May 24,25,26.
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2011-05-20 16:04:30 -04:00 |
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Anton Nekrutenko
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f808de6c90
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Fixes to picard tool intefaces and help sections. Disabled java heap selection by the user (set to 4G default, which was changed in picard_wrapper.py).
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2011-05-20 13:26:45 -04:00 |
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Daniel Blankenberg
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ef795f04e0
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Fix typo (val to value).
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2011-05-20 06:17:35 +01:00 |
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Kelly Vincent
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acb1fbc6f0
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Added hg_g1k_v37 to manual builds
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2011-05-19 15:38:12 -04:00 |
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Jeremy Goecks
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38479cf5c4
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Trackster bug fixes when (a) running tools in a shared visualization and (b) when drawing a track created by a tool.
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2011-05-19 14:29:58 -04:00 |
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Jeremy Goecks
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44beb62a25
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Trackster: have child track inherit mode from parent track.
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2011-05-19 13:47:52 -04:00 |
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Nate Coraor
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b8fd7dbe2e
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Add Picard and fastqc tools to Main
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2011-05-19 10:07:53 -04:00 |
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Jeremy Goecks
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41446bb4b0
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Merge.
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2011-05-18 16:52:38 -04:00 |
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Jeremy Goecks
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c6797482af
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Remove obsolete test values for Cufflinks and Cuffdiff tests.
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2011-05-18 16:52:14 -04:00 |
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Kelly Vincent
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ac95877120
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merge
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2011-05-18 16:51:51 -04:00 |
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Kelly Vincent
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6308d93385
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Further tweaks to Picard help text
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2011-05-18 16:50:37 -04:00 |
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Jeremy Goecks
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8db5b83322
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Clone annotation and tags when cloning workflows.
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2011-05-18 16:48:02 -04:00 |
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Kelly Vincent
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804f9ab60a
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Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible
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2011-05-17 21:31:34 -04:00 |
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Kanwei Li
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d340c2ab22
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Fix data.py typo. Fixes #543
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2011-05-17 18:41:12 -04:00 |
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Ross Lazarus
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c600bed50c
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grr - more vanity attribution removed
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2011-05-17 13:14:15 -04:00 |
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Ross Lazarus
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5096aec964
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cleaned up picard tool names - own section so (picard) was redundant
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2011-05-17 13:04:35 -04:00 |
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Ross Lazarus
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e0545fcd8f
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separated ngs picard tools and removed fastqc wrapper lgpl annotation
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2011-05-17 12:52:24 -04:00 |
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Ross Lazarus
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e5a2a48285
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branch merge with Kelly's fixes
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2011-05-17 12:14:32 -04:00 |
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Daniel Blankenberg
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1dfdc42fe6
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Update tool help for some MAF tools.
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2011-05-17 12:07:25 -04:00 |
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Kelly Vincent
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778088bba9
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Modified Tophat wrapper so dbkey will be properly set both for built-in and history references
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2011-05-17 12:05:07 -04:00 |
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Ross Lazarus
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0aa96d8f0f
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branch merge
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2011-05-17 11:39:52 -04:00 |
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Jeremy Goecks
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2b7025f11d
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Enable Cufflinks to work when setting metadata externally.
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2011-05-17 11:21:26 -04:00 |
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Ross Lazarus
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2e286b5c2d
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amerkinized spelin' and removed copyright notices on some picard tool forms
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2011-05-17 10:29:06 -04:00 |
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Kelly Vincent
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7401ae6439
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Numerous updates to Picard tools: Cleaned up and standardized wrapper's Python code, removing redundant variables and using the same ones in different segment of code when possible; Changed sam/bam outputs to be bam by default and use change_format if user requests sam and removed redundant output parameters; Got tests passing for AddOrReplaceReadGroups; Relaxed the matching constraints for output for BamIndexStats and InsertSize wrappers Standardized on the parameter output-format rather than newformat to indicate sam preference over bam
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2011-05-17 01:57:04 -04:00 |
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Kanwei Li
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5caf51ddaa
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trackster: Refactor LineTrack overflow, fix it to work better for Line and Filled modes
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2011-05-16 17:08:06 -04:00 |
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Ross Lazarus
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6dcd6433e3
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removed python2.4 from rgfakePed.py
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2011-05-16 10:03:47 -04:00 |
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Ross Lazarus
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fa23935ae5
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repairs to rgfakePed tool for generating null genotype data - since removing the _code.py trick of renaming composite file components means all of the parts (eg map and ped) acquire the default name of RgeneticsData, that's what the tool has to create - rather than sensibly named components based on the title - since only way to fix this wart is to reintroduce a bigger wart using the post execution hook, decided to just go with that default base_name to make things more sustanable in the long term
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2011-05-16 09:12:19 -04:00 |
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Ross Lazarus
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7859f56954
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reverting reorder test outputs - PhiX reference used to generate them seems different from that on the buildbot
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2011-05-13 21:24:03 -04:00 |
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Ross Lazarus
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d5fbb00c33
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picard wrapper typo fixed
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2011-05-13 20:46:38 -04:00 |
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Ross Lazarus
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04d6cd3563
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branch merge
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2011-05-13 17:12:44 -04:00 |
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Ross Lazarus
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5e25812f6f
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finally have picard reorder tests working
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2011-05-13 17:12:19 -04:00 |
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Ross Lazarus
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26eaf7a853
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Picard reorder test fix and parameter changes
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2011-05-13 16:54:31 -04:00 |
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Kanwei Li
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3275e4558c
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trackster: tweak resolution, fix LineTrack data bug
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2011-05-13 16:49:43 -04:00 |
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Ross Lazarus
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dfeeecdff8
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Reordersam fails silently if contig names do not match so added an html log where this can be seen easily. Updated insertsize test
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2011-05-13 15:23:32 -04:00 |
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Jeremy Goecks
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649bd62af7
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Trackster: enable chaining of filters.
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2011-05-13 10:02:28 -04:00 |
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Ross Lazarus
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51c28a1a51
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branch merge
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2011-05-13 08:32:35 -04:00 |
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Jeremy Goecks
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4476d5eb00
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Trackster: reset filters when they are hidden.
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2011-05-12 20:01:42 -04:00 |
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Jeremy Goecks
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3eb0c50ae4
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Trackster: enable dynamic filters to be run on complete dataset using filter tools.
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2011-05-12 17:12:01 -04:00 |
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Ross Lazarus
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ecaafc3dff
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more fixes for tests related to new logging method for picard tools
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2011-05-12 16:53:11 -04:00 |
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Ross Lazarus
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75bb1c585f
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branch merge
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2011-05-12 16:48:45 -04:00 |
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Ross Lazarus
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e62a43a621
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update some test outputs for picard
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2011-05-12 16:48:31 -04:00 |
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Kelly Vincent
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c565726192
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Updated help section of BWA wrappers to include tags for the RG header record type
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2011-05-12 13:38:00 -04:00 |
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Daniel Blankenberg
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d69fe3360f
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Add GATK tool-data to buildbot_setup.sh links.
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2011-05-12 12:20:52 -04:00 |
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Daniel Blankenberg
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7b6ee414f0
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Have GATK file listings written as html, be sorted.
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2011-05-12 12:13:18 -04:00 |
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Nate Coraor
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f61df55b8f
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Fix test output for picard_ARRG.
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2011-05-12 11:55:32 -04:00 |
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