USeq Source Code

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.

GATK and Annovar format InDels differently. InDels were labeled 'substitutions', now they are properly labeled insertions and deletions.