AssembleIrysCluster.pl v.1.3 AssembleIrys.pl v.1.2

AssembleIrysCluster.pl Version 1.3 

Fixed bug in lowering minimum lengths. Returned optArguments.xml to default parameters.

AssembleIrys.pl Version 1.2

Fixed bug in lowering minimum lengths
lowered filter length to 100

lowered filter length to 100 and adjusted the format of the commands
script completing update to AssembleIrysCluster.pl Version 1.3
update min length to 100
Switched back to optArguments with triple category

Switched back to optArguments with triple categories after the key
'extensionCommon' was not recognized by assembly pipeline
fix typo in refineassemble script
Update for p-value's position in array
add new parameter "-TE"
specify the extension round
update path to xml
remove the -TE parameter
Adjust default parameters
prep_bnx.pl log file and filenames

prep_bnx.pl now prints a log text file with the run name and the new
molecule bnx filename. prep_bnx.pl also now bumps up the auto increment
value if that file already exists
Create LICENSE.md
Update assembly_qc.pl
Changed style of printing commands
stitch.pl Version 1.1

Separated stitch map from best alignment map. Also generalized
agp2bed.pl.
stitch.pl Version 1.2

stitch.pl Version 1.2 : Check fasta file for redundant super-scaffold
names (this step only effects iterative assemblies), create new AGP,
create a BNG compatible Bed file.
Merge pull request #43 from i5K-KINBRE-script-share/master

stitch.pl Version 1.2