USeq / Source Code Commit Log

Commit	Date
[r301] by biotelerock Lots of mods related to filtering sam alignments for quality to deal with the NextSeq500 data. New features for the simulated tumor sample generation apps.	2015-07-10 22:24:28	Tree
[r300] by biotelerock Made a variety of modifications to support a new app, BamMixer, that wraps a variety of useq apps to generate simulated somatic datasets. Adding in another new app, VCFVariantMaker that generates a vcf file of random snv and indels for use with the BamBlaster app.	2015-06-26 17:16:01	Tree
[r299] by biotelerock Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.	2015-06-19 19:40:00	Tree
[r298] by dnephi Finished CalculatePerCyclePerNucleotideErrorRate. It would be useful to extend this to looking for insertion/deletion errors by position as well, instead of simply providing counts for the number of reads with insertion/deletion events.	2015-06-16 19:23:48	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

[r301] by biotelerock

Lots of mods related to filtering sam alignments for quality to deal with the NextSeq500 data. New features for the simulated tumor sample generation apps.

2015-07-10 22:24:28

Tree

[r300] by biotelerock

Made a variety of modifications to support a new app, BamMixer, that wraps a variety of useq apps to generate simulated somatic datasets. Adding in another new app, VCFVariantMaker that generates a vcf file of random snv and indels for use with the BamBlaster app.

2015-06-26 17:16:01

Tree

[r299] by biotelerock

Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.

2015-06-19 19:40:00

Tree

[r298] by dnephi

Finished CalculatePerCyclePerNucleotideErrorRate. It would be useful to extend this to looking for insertion/deletion errors by position as well, instead of simply providing counts for the number of reads with insertion/deletion events.

2015-06-16 19:23:48

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

USeq Source Code

Source Code Commit Log