USeq Source Code

Added new app to randomly split sam files, mods to MergeSam to filter for bad BamSurgeon reads, removed catch in VCFSample that required read counts for observations (NIST GIB vcfs don't have these).

TomatoFarmer: Graph label changes and pipeline name changes.

Added new app for MergingSam files, a catch for alignments going off the end of chromosomes, updated docs.

TomatoFarmer:
1) Upgraded pipeline to UGP-v1.0.5
2) Can now specify cluster
3) Can now specify full genome analysis
4) Simplified pipeline selection
5) Improved messaging in emails
6) Relaxed pattern matching for fastq files

Bin/Histogram
1) Added support for floating point numbers (needed for full genome)

Sam2USeq
1) Coverage statistics (min/max/median/mean) are now calculated on a histogram instead of an arraylist to avoid running out of memory during full-genome analyses.

Lots of clean up of the documentation and addition of cmd line menu descriptions.

SamTranscriptomeParser: @RG and @PG lines cannot have duplicate ID fields, so STP would crash when merging multiple SAM files. Duplicate ID fields are now suffixed with a number to maintain uniqueness. Modification of the ID field is valid when merging according to SAM spec.

Added lates changes to releaseNotes.txt

Lots of mods to Telescriptor and related classes. Updated DRDS with patch for bad DESeq2 rLog method call.

1. STP bug fix

Latest release notes