Greg Von Kuster 7051ce7dd5 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.

2009-12-08 09:05:35 -05:00

..

pileup_interval.py

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.

2009-12-01 16:18:25 -05:00

pileup_interval.xml

Added the Pileup-to-Interval tool to condense pileup format

2009-09-18 10:15:09 -04:00

pileup_parser.pl

bug fix for pilup_parser reported by user

2009-10-06 09:44:34 -04:00

pileup_parser.xml

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -05:00

sam2interval.py

More SR changes

2009-09-21 10:32:48 -04:00

sam2interval.xml

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

sam_bitwise_flag_filter.py

More SR changes

2009-09-21 10:32:48 -04:00

sam_bitwise_flag_filter.xml

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

sam_merge_code.py

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

2009-08-28 15:59:16 -04:00

sam_merge.py

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

2009-08-28 15:59:16 -04:00

sam_merge.xml

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

2009-08-28 15:59:16 -04:00

sam_pileup.py

Several small changes to Samtools pileup tool to get it to work with user-supplied reference genome

2009-10-05 10:35:39 -04:00

sam_pileup.xml

Corrected Samtools Pileup tool to accept only BAM files as input, instead of also SAM

2009-10-02 09:37:57 -04:00

sam_to_bam.py

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.

2009-12-08 09:05:35 -05:00

sam_to_bam.xml

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.

2009-12-07 16:04:33 -05:00