USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Source Code Commit Log

Commit	Date
[r254] by tmosbruger 1. TomatoFarmer updates 2. SamTranscriptomeParser a) Attempts to report actual chromsome length uses input file header. b) If the chromosome length cannot be found in the input file header, the app will report the last observed position in the chromosome (previous bevior). I c) @RG and @PG lines from input file are maintained 3. AlignmentEndTrimmer: a) Supports hard-clip cigar tag b) Incorporated most recent picard API, which cleaned up some sam validation errors c) Now uses the IH tag to help match pairs when multiple alignments are reported per read. 4) ExportExons a) Exon are named based on gene strand.	2014-09-08 14:26:32	Tree
[r253] by biotelerock Lots of modifications to the Telescriptor app	2014-09-05 21:24:38	Tree
[r252] by biotelerock Telescriptor changes.	2014-08-26 22:08:39	Tree
[r251] by biotelerock More static methods....	2014-08-26 22:08:22	Tree
[r250] by biotelerock Fixed a warning message related to exon size, added methods related to strand.	2014-08-26 22:06:13	Tree
[r249] by biotelerock Mods to support the Telescriptor....	2014-08-26 22:03:54	Tree
[r248] by biotelerock New app and supporting classes for detailed Telescripting discovery.	2014-08-26 22:02:14	Tree
[r247] by biotelerock Added more output options for showing sample names and their order.	2014-08-26 22:01:08	Tree
[r246] by biotelerock Modified default bps to extract alignment counts from 250 to 150. This is a hidden option only used by telescriptors.	2014-08-26 21:59:55	Tree
[r245] by biotelerock Added option to skip alt comparison when scoring matches. Corrected bug where SNP's with two SNP alternates were called nonSNP.	2014-08-26 21:55:54	Tree

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