USeq / Source Code Commit Log

Commit	Date
[r274] by tmosbruger DefinedRegionDifferentialSeq: Changed rLog to rlogTransformation. Apparently rLog is phased out in newer versions TomatoFarmer: Fixed some constant names	2014-12-10 19:29:10	Tree
[r273] by biotelerock Lots of mods related to splice site identification in VCF files, improvements to our bam file QC apps, and extended functionality for comparing VCF files with a relaxed key of BamSurgeon induced variants.	2014-12-04 17:37:17	Tree
[r272] by tmosbruger 1. TomatoFarmer: bug fixes and improvements 2. VCFAnnotator: New annovar versions can be incorporated more easily. 3. MethylationArrayScanner: New option for T-Test 4. SamAlignment: the 'chr' is no longer added to chromosomes. This would cause STP to create two versions of the chromosomes in the header. 5. SamTranscriptomeParser: Relaxed @SQ line matching 6. DefinedRegionDifferentialSeq: Fixed SAMSeq error when there was more than two conditions. New option to turn off DESeq2 independent filtering	2014-12-01 18:49:58	Tree
[r271] by biotelerock Lots of mods....	2014-11-25 17:04:36	Tree
[r270] by biotelerock Adding app to cluster samples in a multi sample vcf file to validate the relationship structure or lack there of.	2014-11-07 22:20:18	Tree
[r269] by codaucious added polyA tag getter	2014-11-03 21:13:47	Tree
[r268] by biotelerock Lots of mods: MultiSampleVCFFilter * Added option to filter by region * Cleaned up chunking issues when no chunking is indicated VarScanVCFParser * New app to extract SOMATIC calls and replace QUAL score with the ssc score. SamAlignmentExtractor * Added option to output alignments that don't intersect the regions. BamSurgeonMutator * Generates random mutations in a list of regions for the BamSurgeon application BisStat * Fixed an issue where some runs were throwing a comparator contract sort error due to lack of data in a particular base context and thus null fraction values	2014-10-30 20:17:09	Tree
[r267] by biotelerock Added option to filter vcfs by region, cleaned un chunking when no chunks called.	2014-10-20 16:45:08	Tree
[r266] by tmosbruger DRDS: Fixed a bug that would report zero counts for the last chromosome in the header when the bam file contains unmapped reads at the end of the file.	2014-10-16 21:30:16	Tree
[r265] by biotelerock Added new app to randomly split sam files, mods to MergeSam to filter for bad BamSurgeon reads, removed catch in VCFSample that required read counts for observations (NIST GIB vcfs don't have these).	2014-10-14 13:52:38	Tree

[r274] by tmosbruger

DefinedRegionDifferentialSeq: Changed rLog to rlogTransformation. Apparently rLog is phased out in newer versions
TomatoFarmer: Fixed some constant names

2014-12-10 19:29:10

Tree

[r273] by biotelerock

Lots of mods related to splice site identification in VCF files, improvements to our bam file QC apps, and extended functionality for comparing VCF files with a relaxed key of BamSurgeon induced variants.

2014-12-04 17:37:17

Tree

[r272] by tmosbruger

1. TomatoFarmer: bug fixes and improvements
2. VCFAnnotator: New annovar versions can be incorporated more easily.
3. MethylationArrayScanner: New option for T-Test
4. SamAlignment: the 'chr' is no longer added to chromosomes. This would cause STP to create two versions of the chromosomes in the header.
5. SamTranscriptomeParser: Relaxed @SQ line matching
6. DefinedRegionDifferentialSeq: Fixed SAMSeq error when there was more than two conditions. New option to turn off DESeq2 independent filtering

2014-12-01 18:49:58

Tree

[r271] by biotelerock

Lots of mods....

2014-11-25 17:04:36

Tree

[r270] by biotelerock

Adding app to cluster samples in a multi sample vcf file to validate the relationship structure or lack there of.

2014-11-07 22:20:18

Tree

[r269] by codaucious

added polyA tag getter

2014-11-03 21:13:47

Tree

[r268] by biotelerock

Lots of mods:

MultiSampleVCFFilter
* Added option to filter by region
* Cleaned up chunking issues when no chunking is indicated
VarScanVCFParser
* New app to extract SOMATIC calls and replace QUAL score with the ssc score.
SamAlignmentExtractor
* Added option to output alignments that don't intersect the regions.
BamSurgeonMutator
* Generates random mutations in a list of regions for the BamSurgeon application
BisStat
* Fixed an issue where some runs were throwing a comparator contract sort error due to lack of data in a particular base context and thus null fraction values

2014-10-30 20:17:09

Tree

[r267] by biotelerock

Added option to filter vcfs by region, cleaned un chunking when no chunks called.

2014-10-20 16:45:08

Tree

[r266] by tmosbruger

DRDS: Fixed a bug that would report zero counts for the last chromosome in the header when the bam file contains unmapped reads at the end of the file.

2014-10-16 21:30:16

Tree

[r265] by biotelerock

Added new app to randomly split sam files, mods to MergeSam to filter for bad BamSurgeon reads, removed catch in VCFSample that required read counts for observations (NIST GIB vcfs don't have these).

2014-10-14 13:52:38

Tree

USeq Source Code

Source Code Commit Log