Initial import.

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@1 fbcdd564-4565-0410-a881-3544ea04ba27
initial checkin

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@2 fbcdd564-4565-0410-a881-3544ea04ba27
initial checkin

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@2 fbcdd564-4565-0410-a881-3544ea04ba27
initial checkin

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@3 fbcdd564-4565-0410-a881-3544ea04ba27
refactored, created intermediate job class with additional methods for output name extraction.

Job -> ECJob -> MapJob (etc)

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@4 fbcdd564-4565-0410-a881-3544ea04ba27
refactored, created intermediate job class with additional methods for output name extraction.

Job -> ECJob -> MapJob (etc)

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@4 fbcdd564-4565-0410-a881-3544ea04ba27
created jar

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@5 fbcdd564-4565-0410-a881-3544ea04ba27
big fixes

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@6 fbcdd564-4565-0410-a881-3544ea04ba27
big fixes

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@6 fbcdd564-4565-0410-a881-3544ea04ba27
wrong arg in pileup -p to -P

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@7 fbcdd564-4565-0410-a881-3544ea04ba27
wrong arg in pileup -p to -P

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@7 fbcdd564-4565-0410-a881-3544ea04ba27
added new processing type CountFastQJob. fixed CountFastQJob (-quals -cycles)

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@8 fbcdd564-4565-0410-a881-3544ea04ba27
added new processing type CountFastQJob. fixed CountFastQJob (-quals -cycles)

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@8 fbcdd564-4565-0410-a881-3544ea04ba27
updated structure of param file

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@9 fbcdd564-4565-0410-a881-3544ea04ba27
updated structure of param file

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@9 fbcdd564-4565-0410-a881-3544ea04ba27
lane specific processing args
new count csv (genComp)
removed readLength Arg

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@10 fbcdd564-4565-0410-a881-3544ea04ba27
lane specific processing args
new count csv (genComp)
removed readLength Arg

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@10 fbcdd564-4565-0410-a881-3544ea04ba27
bug in mapjob, remove "-1" arg to maq

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@11 fbcdd564-4565-0410-a881-3544ea04ba27
bug in mapjob, remove "-1" arg to maq

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX/src@11 fbcdd564-4565-0410-a881-3544ea04ba27
mapjob missing space between args fixed

git-svn-id: https://svn.code.sf.net/p/uscecr/code/WorkflowDAX@12 fbcdd564-4565-0410-a881-3544ea04ba27