Source Code Log

Commit Date  
[r241] by monkeymanstan

Added some new classes, updates to Autoaligner (new sequencing application codes).

2014-06-13 16:34:41 Tree
[r240] by tmosbruger

Deleted TF straggler

2014-06-10 22:32:27 Tree
[r239] by tmosbruger

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

2014-06-04 21:50:20 Tree
[r238] by biotelerock

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.

2014-05-28 20:58:54 Tree
[r237] by biotelerock

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

2014-05-22 20:20:32 Tree
[r236] by biotelerock

Relaxed the thresholds for calling splice damaging/ creating variants.

2014-05-19 14:21:24 Tree
[r235] by biotelerock

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

2014-05-15 20:32:53 Tree
[r234] by biotelerock

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

2014-05-14 21:04:14 Tree
[r233] by biotelerock

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

2014-05-07 22:14:56 Tree
[r232] by biotelerock

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.

2014-05-02 21:35:31 Tree
[r231] by tmosbruger

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.

2014-04-15 19:14:38 Tree
[r230] by tmosbruger

IntersectRegions: Added GC matching functionality. Didn't appear to be implemented in original version
RandomRegions: Did not return null if a region couldn't be found, which caused crashes.

2014-04-09 15:16:38 Tree
[r229] by biotelerock

Added enhancements to the diff splice detection utilities in DRDS including a graph output for diff spliced genes showing the per exon relative log2Rto. Having problems with DEXSeq and a high false positive rate.

2014-04-04 16:10:54 Tree
[r228] by tmosbruger

IntersectRegions: Added support for interval trees
DRDSAnnotator: Added support for multiple rows of annotation for the same gene. Unique entries are concentated and reported.
IntervalTree: Added IntervalTree classes w/ Nix's edits. Added option to search for 'containing' regions intead of intersecting regions

2014-04-01 21:14:14 Tree
[r227] by biotelerock

* Added fix for single stranded lambda datasets, these were crashing the app when calculating the non-conversion rate.
* Added fix for single stranded datasets, this was tossing chromosomes of data that didn't have both a plus and minus strand.
* Added a catch for GQ scores that are floats instead of ints, was causing app to crash.

2014-03-10 19:55:44 Tree
[r226] by biotelerock

Mods to catch null data issues where no vcf records make it through the parsing. This was causing the app to crash out.

2014-03-05 22:59:03 Tree
[r225] by biotelerock

* Bug fix for vcf output where vcf records with no changes were being truncated
* Mods for unsoft masking alignments for IGB visualization

2014-03-05 16:44:53 Tree
[r224] by tmosbruger

ParsePointDataContexts: Fixed bug that would prematurely terminate PPDC if position 7206193 was encountered

2014-02-28 19:55:19 Tree
[r223] by tmosbruger

MergeExonMetrics: Samples are now sorted in alphabetical order
MotifScanner: Motif hit orientation is now reported.

2014-02-28 15:29:45 Tree
[r222] by tmosbruger

RNAEditingPileUpParser: Added option chrM, skips processing chrM

2014-02-27 14:50:42 Tree
[r221] by tmosbruger

Added new app PullMatchingAlignments.
MotifScanner now reports the motif locations in the read.

2014-02-26 22:39:22 Tree
[r220] by biotelerock

Adding zscore support to the VCFSpliceAnnotator

2014-02-22 05:33:25 Tree
[r219] by biotelerock

SamTranscriptomeParser & DefinedRegionDifferentialSeq
* Replaced the IH tag with NH tag for reporting the number of alignments present per read to be compatible with DEXSeq's HTSeq app.

* New app for reducing extreme read depths in amplicon based sequencing datasets

More mods to the SpliceJunction annotator for zscore estimations

2014-02-18 22:21:37 Tree
[r218] by biotelerock

Minor mods to DRDS with option to exclude utr bps from analysis.

2014-02-12 16:34:07 Tree
[r217] by biotelerock

Lots of mods, most are related to changing a method for parsing bed files giving the option to ignore strand.

2014-02-06 17:06:20 Tree
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