USeq / Source Code Commit Log

Commit	Date
[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 BisStat * Added fix for single stranded lambda datasets, these were crashing the app when calculating the non-conversion rate. AllelicMethylationDetector * Added fix for single stranded datasets, this was tossing chromosomes of data that didn't have both a plus and minus strand. VCFComparator * 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 VCFSpliceAnnotator * Bug fix for vcf output where vcf records with no changes were being truncated SamSVFilter * 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

[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

BisStat
* Added fix for single stranded lambda datasets, these were crashing the app when calculating the non-conversion rate.
AllelicMethylationDetector
* Added fix for single stranded datasets, this was tossing chromosomes of data that didn't have both a plus and minus strand.
VCFComparator
* 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

VCFSpliceAnnotator
* Bug fix for vcf output where vcf records with no changes were being truncated
SamSVFilter
* 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

USeq Source Code

Source Code Commit Log