Kelly Vincent a314b3716b 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

..

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

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.

2010-01-14 14:07:05 -05:00

pileup_parser.xml

Small edit for the help section

2010-01-14 14:20:01 -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 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_pileup.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_pileup.xml

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_to_bam.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_to_bam.xml

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