 Greg Von Kuster
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7051ce7dd5
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Rename the before_edit() and after_edit() metadata related methods to be more appropriately named before_setting_metadata() and after_setting_metadata(), and add the metthods to all datatype classes. Move sorting of Bam files from the Bam set_meta() method to this new method.
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2009-12-08 09:05:35 -05:00 |
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Greg Von Kuster
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bcd6751cdf
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Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
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2009-12-07 16:04:33 -05:00 |
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Greg Von Kuster
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08e0d5e532
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Fixes for Bam data type's set_meta() and sam_to_bam tool, indexes will now be properly created for bam datasets. Fixes also for uploading Bam files, they will no longer be uncompressed on upload.
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2009-12-04 19:51:46 -05:00 |
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Kelly Vincent
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606ac644f3
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Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa.
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2009-12-01 16:18:25 -05:00 |
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Kelly Vincent
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0a51932168
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Changed sam-to-bam test by removing nonexistent dbkey from test input specification.
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2009-11-11 13:53:48 -05:00 |
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Nate Coraor
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56032de2bd
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Upgrade to Cheetah 2.2.2
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2009-11-10 13:47:34 -05:00 |
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Kelly Vincent
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8879adc01e
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Commented out second test for SAM-to-BAM so tests will pass, because it relies on using a built-in dbkey that doesn't exist in builds.txt
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2009-11-06 16:52:00 -05:00 |
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Anton Nekrutenko
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7189873b59
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bug fix for pilup_parser reported by user
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2009-10-06 09:44:34 -04:00 |
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Kelly Vincent
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0ffbe38fc3
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Several small changes to Samtools pileup tool to get it to work with user-supplied reference genome
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2009-10-05 10:35:39 -04:00 |
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Kelly Vincent
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5c94d0c273
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Corrected Samtools Pileup tool to accept only BAM files as input, instead of also SAM
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2009-10-02 09:37:57 -04:00 |
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Kelly Vincent
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ef2ef943ea
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Fixed an error in the help section of the Sam Pileup tool config
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2009-09-25 16:49:30 -04:00 |
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Anton Nekrutenko
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2e7fdf2bff
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Added Cite to masthead
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2009-09-25 13:58:15 -04:00 |
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Kanwei Li
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a947686b77
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fix some typos for tools in folders N-Z
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2009-09-25 02:06:03 -04:00 |
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Anton Nekrutenko
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b93db2deff
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small help and parameter name tweaks
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2009-09-24 11:55:55 -04:00 |
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Anton Nekrutenko
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cb635b8148
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Tweaks plus reducing size of Assaf's icons
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2009-09-21 15:40:22 -04:00 |
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Anton Nekrutenko
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8d0e39c9f8
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More SR changes
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2009-09-21 10:32:48 -04:00 |
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Anton Nekrutenko
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eaed01bcf4
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First pass of consolidating NGS tools
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2009-09-18 10:27:03 -04:00 |
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Kelly Vincent
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be211aa254
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Added the Pileup-to-Interval tool to condense pileup format
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2009-09-18 10:15:09 -04:00 |
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Anton Nekrutenko
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75ce85cd3f
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Added sam2interval converter
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2009-09-16 16:00:09 -04:00 |
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Anton Nekrutenko
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b833f1819d
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A tool for filtering SAM datasets on bitwise flag.
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2009-09-16 15:19:35 -04:00 |
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Anton Nekrutenko
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61c7d63087
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Added pileup parser. Pardon the perl = used to its regexes too much
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2009-09-04 10:23:37 -04:00 |
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Kelly Vincent
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1008d8692f
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Added several options to the Samtools pileup tool
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2009-09-01 17:01:44 -04:00 |
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Kelly Vincent
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9d0dd5f7ce
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Added samtools-based tools (sam_to_bam, sam_merge, sam_pileup) with their supporting files and modified Bam datatype so temp files are properly cleaned up
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2009-08-28 15:59:16 -04:00 |
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