Kelly Vincent 5c546a21b3 Updating sam_indel_filter tool; adding NGS: Indel Analysis section; adding indel_analysis, indel_table, and indel_sam2interval tools

2010-07-14 01:09:52 -04:00

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pileup_interval.py

Sync hashbangs

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

pileup_interval.xml

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

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

pileup_parser.pl

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

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 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 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

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

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

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

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