USeq Source Code

1. Fixed issue where analysis# = null in cmd.txt when multiple samples from the same experiment number listed
2. Fixed an issue where Tomato couldn't find the newly created analysis report to drop in the log.txt file.
3. Fixed error where Tomato couldn't find the appropriate jobs dir for subsamples.
4. Added more sequencing application codes to the list of abbreviated codes
5. Fixed error with moving parsed fresh data report to processedReports folder.
6. Changed code to soft link input fastq files instead of specifying full path (Tomato doesn't allow calling full path)

Updated regex string to match exception cases for genome build as reported by GNomEx

Fixed location of directory for httpclient_create_analysis.sh that calls createAnalysisMain

Fixed index out of bounds bug when input fresh data report is missing expected column.

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