Kelly Vincent 44fb42f6a0 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.

2010-03-10 11:51:00 -05:00

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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

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

pileup_parser.xml

Modifications to pileup_parser

2010-03-02 16:35:21 -05:00

sam2interval.py

Have sam2interval provide a (partial) header so that strand is automatically set in metadata.

2010-02-05 11:53:06 -05:00

sam2interval.xml

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00

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

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.

2010-02-23 10:40:19 -05:00

sam_merge.xml

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.

2010-02-24 07:11:43 -05:00

sam_pileup.py

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.

2010-03-10 11:51:00 -05:00

sam_pileup.xml

Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass

2010-02-25 23:20:19 -05:00

sam_to_bam.py

Fix locations of cached data for tests

2010-02-25 12:27:07 -05:00

sam_to_bam.xml

Fixed dbkey's in sam_pileup and sam_to_bam tools in tests so they will pass

2010-02-25 23:20:19 -05:00