USeq Source Code

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

Added InosinePredict to build for the Bass lab

DRSS reports maximum coverage position when run on a single dataset.

1. Fixed bug with matching entire output string from create_analysis_main for new analysis report dir path

1. Added code to parse out versioned genome and store in Sample object field
2. Alignments run through SamTranscriptomeParser after alignment
2. Added flag to reverse strand in STP if paired-end && sequencingApplicationCode = APP2/APP3
3. Added functionality to run all input fastq files through fastqc prior to aligning
4. Added code to create relative read coverage tracks using the Sam2USeq app
5. Added code to run genomic alignments through CalculatePerCycleErrorRate
6. Fixed bug where new Analysis Report dir was not created