USeq Source Code

Lots of mods to support the processing of methylated datasets where particular chromosomes only have + or - stranded data and not both. This breaks most everything. Ugg.

Added new beta app for annotating vcf variants with splice junction affects.

Bug Fix

Added ability to set the minimum base read coverage threshold, defaults to 5 alignments

Added support for David's best practices to TomatoFamer. See 'exome_best'

DefinedRegionDifferentialSeq
* Fixed bug when DESeq was outputting FDRs with "NA", these were being assigned the max FDR, switched it to 0.
Note, this won't effect most analysis since these genes also have a log2 of 0 and wouldn't survive standard log2Ratio thresholding.

NovoalignBisulfiteParser
* Fixed a bug in the -b4 novoalignment parsing
* Remove support for native novoalign format, just sam/ bam now.

Updates to bisulfite processing to support -b4 novoalignments, reinstatement of overlapping paired read collapsing, additions to VCF classes to allow for scoring splice junction effects.

Updates to the docs with current best practices.

Added some test sequence files with examples for running through the MaxEntScan apps.

Updated with latest changes