USeq Source Code

Did a bunch of reorganization and merging of vcf related classes under edu/utah/seq/vcf

Added new app for filtering multi sample vcf files. Set sam parser stringency on DRDS to silent. More gzipper options.

New app for RNAEditing, mods to AggregatePlotter to catch bad region files

Cleaned up commented debugging code

Added FDR estimation to RNAEditing apps

Fixed the wording of the help menu.

Added changes for 5.8.1

Lots of mods:
MergePairedSamAlignments
* Fixed bug when merging bam files where double line returns where causing Picard's SortSam to error out.
VCFTabix
* New app for recursing through directories and tabix indexing vcf files
USeq2UCSCBig and UCSCBig2USeq
* Added new options for skipping for forcing overwrite of already converted files
* Added options to silence all but error messages
CalculatePerCycleErrorRate
* Added ability to work with unsorted sam files
* Added option to require read names start with a given prefix. Novoalign is adding in some junk reads to their output?
MergeUCSCGeneTable
* Fixed bug where 1bp terminal exons were being skipped causing the conversion of bed12 useq files to bb to throw an error.
SamTranscriptomeParser
* Fixed bug where insertions or deletions that occurred at the splice junction were causing the failure to insert an appropriate number of Ns