v0.0.9 Feb 13, 2015

Changed how statistics are printed out. Changed chimeric script to be a blacklist instead of whitelist. Removed unnecessary files.

BioScripts 3d15edc9eadc3172905dfd0a683e7cf20b5000f0

v0.0.8 Nov 18, 2014

Fixed off by one bug in chimeric.awk and added support for other names for chromosomes; added in MAPQ filter in statistics.pl and in base Java class; added support in split_rmdups for more splits than usual; added some new key information into properties; changed how LibraryComplexity is called.

BioScripts ff695c9bf45d062aff03316a1350dfc235752b15

v0.0.7 Apr 3, 2014

Adjust abnormal script. Add early exit to align script. Add comments to everything. Cleanup when jobs fail in launch.

svn r135

v0.0.6 Nov 29, 2013

Different default for fragment.pl; comment in statistics.pl; changed what we print out for abnormal.txt

svn r130

v0.0.5 Jul 18, 2013

Add the about option to the pipeline. Changed align and launch scripts to be compatible with streaming change to statistics.pl. Also added flags for adding description and parenthetical to MiSeq with read counts. Added script to cleanup after pipeline runs

svn r118

v0.0.4 Jul 11, 2013

Changed default restriction enzyme. Changed how we look for optical duplicates
svn r114

v0.0.3 May 1, 2013

Keep unmapped reads in a separate file.
svn r110

v0.0.2 Apr 17, 2013

Added in key for properties menu
LibraryComplexity reads files to calculate unique read pairs / duplicates
Name of optical dups file changed
Got rid of Matlab for producing graphs (affects launch, statistics, and relaunch), Java now reads the .m file directly and produces them in the Juicebox GUI
Mapq script now also eliminates intra fragment reads
svn r107

v0.0.1 Mar 8, 2013

Initial commit