USeq Source Code

Modified code to move parsed fresh data report

Updated directories, modified mv function for parsed fresh data reports, fixed a few other random bugs

Fixed Ant script. USeq archive is now unzipped to USeq folder instead of root directory.

Lots of modifications to catch errors associated with converting bed12 useq files to bb.

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.