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
