USeq Source Code

Initial check-in of Ames data.

Primary change is to catch a bug with MergeParedSamAlignments from xxx.bam files leading to a double return in the temp output that then crashes the Picard SortSam

Lots of mods to support silent execution and only print errors so this can be run as a cron job. Modified all apps to only convert files that haven't been converted unless the -f force flag is given.

Added option to delete uncompressed vcf files and force rewriting existing indexes

Added new app that wraps the VCF tabix conversion for GNomEx auto conversions, updated the build.properties and applications.html

Fixed classpath error. Shouldn't have to extract 3rd part jar file anymore to complete document target.

New app CalculatePerCycleErrorRate, mod to MergePairedSamAlignments to skip merging phiX, new methods to Num, updated releaseNotes and the build.properties.

Added util/apps/CompareIntersectingRegions app to jar list

Fixed and issue where adjacent regions were pulling the same reads that then would both get written to file producing dups.