USeq Source Code

Updates to bisulfite processing to support -b4 novoalignments, reinstatement of overlapping paired read collapsing, additions to VCF classes to allow for scoring splice junction effects.

Updates to the docs with current best practices.

Added some test sequence files with examples for running through the MaxEntScan apps.

Updated with latest changes

Added Java implementations of Yeo and Burge's Max Ent Scan algorithms for human splice site detection

VCFAnnotator: This app now supports VAAST 2.0 output, including InDels

SRAProcessor
* Added option to set quality score offset to 64, needed for some Illumina datasets
MiRNACorrelator
* Added ggplot2 box whisker plot functionality

TomatoFarmer: Implement deleteing intermediate bams
TFCommandExomeVariant: Fixed chunking behavior when inverval exactly matches remaining chunk space. This produced a zero length interval, which GATK dislikes.

Updated docs for chIPSeq and RNASeq.

MultiSampleVCFFilter: Allow strict genotype matching, which drops records with missing genotypes.