USeq Source Code

Adding zscore support to the VCFSpliceAnnotator

SamTranscriptomeParser & DefinedRegionDifferentialSeq
* Replaced the IH tag with NH tag for reporting the number of alignments present per read to be compatible with DEXSeq's HTSeq app.

SamReadDepthSubSampler
* New app for reducing extreme read depths in amplicon based sequencing datasets

More mods to the SpliceJunction annotator for zscore estimations

Minor mods to DRDS with option to exclude utr bps from analysis.

Lots of mods, most are related to changing a method for parsing bed files giving the option to ignore strand.

ExportExons: Added option to report GENENAME_EXONNUMBER in bed file name column (-n). This allows you to use the resulting bed in the DRDS application.
PairedCondition: This was modified to support SAMseq, should have been included in last check-in

DRDS: Added support for SAMseq. Use the option -a to run. Won't run if there aren't at least two replicates in each condition.
RNASeq: Added option to run SAMseq. Use option -q to run.

ScanSeqs: Fixed bug where reduced region q-values were not zeroed out when the number of observations is less than 21 and only enriched regions are being tested. The reduced region p-value would remain in the place of the q-value, which mostly affects q-value datatrack creation.

DRDSAnnotator now splits first column by "_". Won't affect Ensembl IDs, but will allow annotation of refflat files with the format ENSEMBL_GENENAME.

1. catch when genome build specified as H_sapiens_Jun_2013 (B37) for RNA-Seq data; change to hg19

1. reset serverURL for createAnalysisMain to bioserver. It isn't working with Apache Tomcat.
2. changed code to require config file with run parameters