Kanwei Li ba597f99d7 Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria

2010-11-13 14:37:26 -05:00

..

bam_to_sam.py

Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers

2010-11-08 15:00:54 -05:00

bam_to_sam.xml

Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers

2010-11-08 15:00:54 -05:00

pileup_interval.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

pileup_interval.xml

Requirements tags for some samtools tools

2010-09-26 18:06:01 -04:00

pileup_parser.pl

Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.

2010-04-14 13:52:35 -04:00

pileup_parser.xml

changes to help text

2010-04-15 11:10:57 -04:00

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

Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria

2010-11-13 14:37:26 -05:00

sam_bitwise_flag_filter.xml

Minimally functional splitting.

2010-11-10 12:06:05 -05:00

sam_merge_code.py

Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

2010-09-27 21:35:03 -04:00

sam_merge.py

Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output

2010-04-12 15:56:13 -04:00

sam_merge.xml

Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers

2010-11-08 15:00:54 -05:00

sam_pileup.py

Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output

2010-04-12 15:56:13 -04:00

sam_pileup.xml

Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers

2010-11-08 15:00:54 -05:00

sam_to_bam.py

Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.

2010-04-30 15:27:41 -04:00

sam_to_bam.xml

Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers

2010-11-08 15:00:54 -05:00