 Dannon Baker
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39eb262219
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More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16
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2016-02-02 13:54:24 -05:00 |
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Dannon Baker
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ba9ad97c40
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Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details.
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2016-02-02 09:30:30 -05:00 |
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John Chilton
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2b02677e85
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Workaround for metadata_bam.xml failure.
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2015-09-19 10:27:09 +01:00 |
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Greg Von Kuster
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8ba7de4c8b
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Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
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2011-03-23 12:18:57 -04:00 |
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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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