USeq / Source Code Commit Log

Commit	Date
[r297] by biotelerock Sam2USeq: Fixed an issue where chromData from the MergePairedAlignments app fail to calc read coverage with b37 no "chr" data. Now must match the bed file with the alignments. PoReCNV: change the way loaded data is saved to enable per sample loading for additional runs. VCF mods to support parsing of LoFreq's crazy vcf format New app for converting a bed file to a gene table by intersecting it with another gene table.	2015-06-06 14:29:23	Tree
[r296] by biotelerock OK: 1) updating the .project file and the new way Eclipse creates faceted projects. Hopefully this minimize the hell of getting USeq installed in Eclipse 2) Added some mods to the CollectBamStats app to skip particular parsing if the log file doesn't have it 3) Added Z-Score calcs, graphs, and xls and bed output to PoReCNV to help in calling real CNVs	2015-05-27 17:04:00	Tree
[r295] by dnephi Made a number of changes as I'm writing the read pair flattener for barcoded reads.	2015-05-15 23:00:56	Tree
[r294] by tmosbruger Read lengths are calculated using the reported sequence vs perfect cigar. This avoids crashes when there are very few reads.	2015-04-21 23:12:12	Tree
[r293] by biotelerock Added functionality to PoReCNV to join adjacent passing exons into larger CNV block.	2015-04-15 21:38:06	Tree
[r292] by biotelerock Fixed an issue with PoReCNV where the last chromosome of data wasn't being processed when batching R calls.	2015-04-03 15:23:29	Tree
[r291] by tmosbruger All TF commands now report available diskspace in the stdout.txt file.	2015-04-01 17:06:11	Tree
[r290] by tmosbruger Sam2USeq: Prepend chr to bed regions, if it isn't there already. TomatoFarmer: TomatoFarmer now injects a script into each cmd.txt file that determines the memory, cpus and GCThread count. Before the resources were set to the specs of the weakest nodes in our clusters. The commands also now report the the node that ran the job, which should help with future debugging. VCFAnnotator: Added CADD scores, improved the genotype reporting in the last set of columns. VCFAnnotator should now work with FreeBayes output.	2015-04-01 14:30:26	Tree
[r289] by biotelerock Dropped support for unsorted sam.gz files, this was causing issues with files that had no phiX	2015-03-17 20:20:17	Tree
[r288] by biotelerock Lots of mods to the individual VCF parsers to standardize them for merging with Somatic variant analysis. More mods to the PoReCNV app. Fixed an issue with the CollectBamStats where changes to the default thresholds were being overwritten.	2015-03-17 16:55:08	Tree

[r297] by biotelerock

Sam2USeq: Fixed an issue where chromData from the MergePairedAlignments app fail to calc read coverage with b37 no "chr" data. Now must match the bed file with the alignments.

PoReCNV: change the way loaded data is saved to enable per sample loading for additional runs.

VCF mods to support parsing of LoFreq's crazy vcf format

New app for converting a bed file to a gene table by intersecting it with another gene table.

2015-06-06 14:29:23

Tree

[r296] by biotelerock

OK:
1) updating the .project file and the new way Eclipse creates faceted projects. Hopefully this minimize the hell of getting USeq installed in Eclipse
2) Added some mods to the CollectBamStats app to skip particular parsing if the log file doesn't have it
3) Added Z-Score calcs, graphs, and xls and bed output to PoReCNV to help in calling real CNVs

2015-05-27 17:04:00

Tree

[r295] by dnephi

Made a number of changes as I'm writing the read pair flattener for barcoded reads.

2015-05-15 23:00:56

Tree

[r294] by tmosbruger

Read lengths are calculated using the reported sequence vs perfect cigar. This avoids crashes when there are very few reads.

2015-04-21 23:12:12

Tree

[r293] by biotelerock

Added functionality to PoReCNV to join adjacent passing exons into larger CNV block.

2015-04-15 21:38:06

Tree

[r292] by biotelerock

Fixed an issue with PoReCNV where the last chromosome of data wasn't being processed when batching R calls.

2015-04-03 15:23:29

Tree

[r291] by tmosbruger

All TF commands now report available diskspace in the stdout.txt file.

2015-04-01 17:06:11

Tree

[r290] by tmosbruger

Sam2USeq: Prepend chr to bed regions, if it isn't there already.
TomatoFarmer: TomatoFarmer now injects a script into each cmd.txt file that determines the memory, cpus and GCThread count. Before the resources were set to the specs of the weakest nodes in our clusters. The commands also now report the the node that ran the job, which should help with future debugging.
VCFAnnotator: Added CADD scores, improved the genotype reporting in the last set of columns. VCFAnnotator should now work with FreeBayes output.

2015-04-01 14:30:26

Tree

[r289] by biotelerock

Dropped support for unsorted sam.gz files, this was causing issues with files that had no phiX

2015-03-17 20:20:17

Tree

[r288] by biotelerock

Lots of mods to the individual VCF parsers to standardize them for merging with Somatic variant analysis.

More mods to the PoReCNV app.

Fixed an issue with the CollectBamStats where changes to the default thresholds were being overwritten.

2015-03-17 16:55:08

Tree

USeq Source Code

Source Code Commit Log