USeq Source Code

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

Source Code Commit Log

Commit	Date
[r104] by tmosbruger Added option -b to both SamTranscriptomeParser and RNASeq. This option flips the strand of both reads. Note that this is independent of the flip second strand option, selecting both will leave the second strand read unchanged.	2013-04-24 16:13:57	Tree
[r103] by biotelerock Added option for stranded analysis into DefinedRegionRNAEditing	2013-04-18 20:23:35	Tree
[r102] by biotelerock Added options for stranded analysis to the RNAEditing apps Mods to the VCFComparator and VCFRecord to deal with odd vcf files Updated the release notes	2013-04-17 22:16:14	Tree
[r101] by biotelerock Added VCFComparator and Sam2USeq notes	2013-04-09 16:07:48	Tree
[r100] by biotelerock Added mean, median, min, max stats for coverage over interrogated regions	2013-04-09 16:01:48	Tree
[r99] by biotelerock Added methods for working with short[]	2013-04-09 16:01:32	Tree
[r98] by tmosbruger Bug fixes and improvements to VCFAnnotator, VCFComments and VCFReporter	2013-04-05 20:19:45	Tree
[r97] by tmosbruger added apps to build file	2013-04-05 16:06:28	Tree
[r96] by tmosbruger VCFAnnotator: Added new annotations and better descriptions. VCFReporter: Merged VCFToTable and VCFInfoEdit into one app VCFUtilites: Creates/Uncompresses tabix vcf files. Lots of other small changes.	2013-04-05 16:01:31	Tree
[r95] by tmosbruger Added ParseExonMetrics, which takes the output from several sequencing diagnostic programs and creates PDF containing all of them. Several mods to existing Apps to support tomato v2. Added GenerateOverlapStats, which generates the same metrics as MergePairedSamAlignments, but does not require the time-intensive sort or sam manipulations.	2013-04-02 20:55:14	Tree

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