Update to stitch.pl v.1.3

Die and report when no super scaffolds can be found. Give generic names
to contigs. Check for IUPAC ambiguous bases other than n when making
AGP.
Update stitch.pl

Update notifications
Update stitch.pl

Update doc
Update clusterArguments.xml

Modified to fit the 06/25/14 update to Assembler and RefAligner.
Software upgrade clusterArguments.xml

Modified to fit the 06/25/14 update to Assembler and RefAligner.
Update OptArguments2.xml

Updated to new pipeline
Update assemble.pl

Updated for new pipeline
Update RefineAssembleIrys.pl
AssembleIrysCluster.pl v. 1.4

Updated for new Assembler with auto noise
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Update RefineAssembleIrys.pl
Update clusterArguments.xml
Update mic jobs
correct xml parse step
Update assemble.pl
Update assemble.pl
Switch to regex for optArgument.xml editing
fixed typo in regex
regex fix
Update assemble.pl