USeq Source Code

Modified default bps to extract alignment counts from 250 to 150. This is a hidden option only used by telescriptors.

Added option to skip alt comparison when scoring matches. Corrected bug where SNP's with two SNP alternates were called nonSNP.

AlignmentEndTrimmer
Bug fix: mismatches are now counted properly on the reverse strand
VCFParser
Added support for awful varcsan VCF output.

AllelicExpressionDetector
* Application for identifying allelic expression based on a table of snps and bam alignments filtered for alignment bias (see ReferenceMutator and SamComparator).
ReferenceMutator
* Given a table of snps and directory of reference fasta files. Introduces the non reference base into the fastas.
DefinedRegionDifferentialSeq
* Added option to collect counts from the 5' and 3' ends of genes
DifferentialReadCoverageComparator
* Takes the count table generated by DRDS with the -z option and looks for changes in 5'/3' read coverage between different conditions to identify short truncated transcripts
RandomMutationGenerator
* Creates snvs and indels for the BAMSurgeon application

AlignmentEndTrimmer: Option -s added to drop reads with -x number of mismatches. If option -e is specified, RNA editing changes are ignored.

Added some new classes, updates to Autoaligner (new sequencing application codes).

Deleted TF straggler

TomatoFarmer Overhaul
1) Works with pysano
2) Code is more organized
3) Can result incomplete jobs
4) Only recalibrates by sample (not by lane)

Updated picard jars. They did a big package rearrangement so had to modify a bunch of classes. Might be a bit painful to get stuff fixed.

Modified RNASeq app to use DESeq2 for the scanning and gene analysis