USeq Source Code

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.

DefinedRegionDifferentialSeq
* Added a System.setProperty("java.awt.headless", "true") to allow running app in non x11 mode.

VCFSample
* Changed how it recognizes a no call to anything that starts with ./. so these are skipped

FilterIntersectingRegions
* Added option to split gtf/ gff files

*Added support for BWA mem. This broke some of the USeq apps that expect a single alignment per pair and didn't check the primary flag.
*Remove hard-coded paths to software and added them to the config file. I don't like a user-specified config file... I need to come up with a better solution
*Changed the names of the output VCF files, 'filtered' and 'passing' was too cryptic. Files are now 'filterFieldSetAll' and 'filterFieldSetPassing', much clearer?
*Merged 'primary' and 'padded' target bed file and added AgilentV5UTR to list.