USeq Source Code

Deleted TF straggler

TomatoFarmer Overhaul
1) Works with pysano
2) Code is more organized
3) Can result incomplete jobs
4) Only recalibrates by sample (not by lane)

Updated picard jars. They did a big package rearrangement so had to modify a bunch of classes. Might be a bit painful to get stuff fixed.

Modified RNASeq app to use DESeq2 for the scanning and gene analysis

Relaxed the thresholds for calling splice damaging/ creating variants.

Brought the RNASeq, ChIPSeq, and MultipleReplicaScanSeqs up to speed with DESeq2

Switched the default behavior to merge stranded datasets. These plus minus useq files were causing all kinds of grief.

Cleaned up the code in the VCFComparator. Put in some more catches for NA and INF vals coming back from R

Lots of clean up.
Updated DRDS to DESeq2: major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.

AlignmentEndTrimmer: This application can be used to trim alignments according to the density of mismatches. Each base of the alignment is compared to the reference sequence from the start of the alignment to the end. If the bases match, the score is increased by -m. If the bases don't match, the score is decreased by -n. The alignment position with the highest score is used as the new alignment end point. The cigar string, alignment position, mpos and flags are all updated to reflect trimming.