USeq Source Code

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

Autoaligner
1. Fix regexs to more explicitly match versioned genome, build code, and both paired-end fastq files
2. Modified build code and versioned genome to set as lower case to match case of approved index names
3. Fixed a bug that would print an error to log (saying dir wasn't created) when a new analysis report directory was created
4. Updated server URL for createAnalysisMain to hci-bio-app
5. Fixed logging errors
6. Added more new sequencing application codes
7. Logs now report how each sample is handled
Sample
1. added getters/setters for a number of new booleans

Initial commit of DRDSAnnotator

MicrosatelliteCounter: Added new options and will now skip reads with unterminated repeats