 Kelly Vincent
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5c546a21b3
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Updating sam_indel_filter tool; adding NGS: Indel Analysis section; adding indel_analysis, indel_table, and indel_sam2interval tools
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2010-07-14 01:09:52 -04:00 |
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Kelly Vincent
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862531e04e
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Changed the way sam_indel_filter expects quality score cutoffs and fixed bug so it checks qualities for correct bases in all cases
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2010-06-24 13:43:38 -04:00 |
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Kelly Vincent
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7373e78cd4
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Fixed handling of alignments with CIGAR strings with multiple indels for SAM indel filter, plus updated test files
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2010-06-10 13:19:43 -04:00 |
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Kelly Vincent
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78b17cbb9c
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Adding SAM indel filter tool with test files
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2010-06-07 15:23:32 -04:00 |
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Kelly Vincent
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139c2cf667
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Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.
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2010-04-30 15:27:41 -04:00 |
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Anton Nekrutenko
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008cc9a012
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changes to help text
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2010-04-15 11:10:57 -04:00 |
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Anton Nekrutenko
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254ad33d95
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Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.
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2010-04-14 13:52:35 -04:00 |
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Kelly Vincent
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eeca0c723a
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Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output
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2010-04-12 15:56:13 -04:00 |
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Anton Nekrutenko
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04ed0933cf
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Updated output format for solid2fastq converter
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2010-04-07 08:44:57 -04:00 |
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Kanwei Li
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0952b28502
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Sync hashbangs
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2010-04-01 20:36:31 -04:00 |
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Kelly Vincent
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38ad670389
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Updated several NGS tools to better handle stderr (allow for extremely large stderr output)
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2010-03-30 16:33:19 -04:00 |
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Kelly Vincent
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44fb42f6a0
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Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling.
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2010-03-10 11:51:00 -05:00 |
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Anton Nekrutenko
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175c63e0fd
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Modifications to pileup_parser
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2010-03-02 16:35:21 -05:00 |
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Kelly Vincent
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d091640cb5
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Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass
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2010-02-25 23:20:19 -05:00 |
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Nate Coraor
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0bfa58679b
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Fix locations of cached data for tests
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2010-02-25 12:27:07 -05:00 |
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Kelly Vincent
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09fa3f0bf1
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Updated Bowtie test files to handle new version (0.12.3) of Bowtie (bowtie_color_wrapper will fail until new version installed). Updated samtools tools test files. Removed version references from Bowtie and BWA tools.
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2010-02-24 07:11:43 -05:00 |
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Kelly Vincent
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a314b3716b
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Updated BWA wrapper, SAM to BAM, SAM Merge, and SAM Pileup so that the return code of the program is captured and if it fails, the stderr is printed; temp files are created locally; a message is printed if results file empty.
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2010-02-23 10:40:19 -05:00 |
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Daniel Blankenberg
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37ae9ac29d
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Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.
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2010-02-05 16:06:27 -05:00 |
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Daniel Blankenberg
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561f0abf75
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Have sam2interval provide a (partial) header so that strand is automatically set in metadata.
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2010-02-05 11:53:06 -05:00 |
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Anton Nekrutenko
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540cfb1931
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Small edit for the help section
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2010-01-14 14:20:01 -05:00 |
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Anton Nekrutenko
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a4361dcce1
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Modification of pileup filter behavior, bases not different from the references are included in the report as well. Also changed the image for closing screencast panels. A new icon is urgently needed.
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2010-01-14 14:07:05 -05:00 |
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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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