USeq Source Code

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

Adding in changes for Misc and Num.

1. TomatoFarmer updates
2. SamTranscriptomeParser
a) Attempts to report actual chromsome length uses input file header.
b) If the chromosome length cannot be found in the input file header, the app will report the last observed position in the chromosome (previous bevior). I
c) @RG and @PG lines from input file are maintained
3. AlignmentEndTrimmer:
a) Supports hard-clip cigar tag
b) Incorporated most recent picard API, which cleaned up some sam validation errors
c) Now uses the IH tag to help match pairs when multiple alignments are reported per read.
4) ExportExons
a) Exon are named based on gene strand.