Source Code Log


Commit Date  
[r213] by tmosbruger

DRDSAnnotator now splits first column by "_". Won't affect Ensembl IDs, but will allow annotation of refflat files with the format ENSEMBL_GENENAME.

2014-01-22 15:50:12 Tree
[r212] by monkeymanstan

1. catch when genome build specified as H_sapiens_Jun_2013 (B37) for RNA-Seq data; change to hg19

2014-01-14 23:12:17 Tree
[r211] by monkeymanstan

1. reset serverURL for createAnalysisMain to bioserver. It isn't working with Apache Tomcat.
2. changed code to require config file with run parameters

2014-01-14 21:40:44 Tree
[r210] by monkeymanstan

Autoaligner
1. Fix regexs to more explicitly match versioned genome, build code, and both paired-end fastq files
2. Modified build code and versioned genome to set as lower case to match case of approved index names
3. Fixed a bug that would print an error to log (saying dir wasn't created) when a new analysis report directory was created
4. Updated server URL for createAnalysisMain to hci-bio-app
5. Fixed logging errors
6. Added more new sequencing application codes
7. Logs now report how each sample is handled
Sample
1. added getters/setters for a number of new booleans

2014-01-13 22:25:39 Tree
[r209] by tmosbruger

Initial commit of DRDSAnnotator

2014-01-10 21:55:44 Tree
[r208] by tmosbruger

MicrosatelliteCounter: Added new options and will now skip reads with unterminated repeats

2014-01-09 16:05:29 Tree
[r207] by biotelerock

Added latest apps.

2014-01-08 16:34:02 Tree
[r206] by biotelerock

Latest mods for associating variants with splice junctions.

2014-01-08 16:32:36 Tree
[r205] by tmosbruger

Added new MicrosatelliteCounter application.
Made small changes to the BisSeqAggregatePlotter and Gr2Bar apps.

2014-01-06 18:49:20 Tree
[r204] by monkeymanstan

Added an option to first call Picard's SortSam and MarkDuplicates

2014-01-06 18:17:11 Tree
[r203] by monkeymanstan

Wrapper for Picard's MarkDuplicates

2014-01-06 18:02:18 Tree
[r202] by biotelerock

Mods to STP to output just spliced alignments.
Mods to VCFAnnotator to convert scores to pvalues.
Mods to MiRNACorrelator to improve ggplot scripts.

2014-01-04 00:15:40 Tree
[r201] by monkeymanstan

Added an option to first call Picard's SortSam and MarkDuplicates. This is a critical step in parsing bisulfite data, as the percentage of duplicate reads can be quite high!

2013-12-30 22:33:45 Tree
[r200] by biotelerock

Added indel support to the VCFSpliceAnnotator

2013-12-30 22:08:30 Tree
[r199] by biotelerock

* Added a catch to skip calculating stats on bins with only one value
* Fixed bug with the ordering of the bins in the ggplot

2013-12-23 17:22:25 Tree
[r198] by biotelerock

Added new SamSVFilter app to build

2013-12-20 17:21:53 Tree
[r197] by biotelerock
2013-12-20 17:19:48 Tree
[r196] by biotelerock

Backed out Darrens changes until these are optional

2013-12-20 17:16:28 Tree
[r195] by tmosbruger
2013-12-18 00:00:59 Tree
[r194] by tmosbruger

MultiSampleVCFFilter: Bug fix, the behavior of -M was incorrect.

2013-12-16 17:32:59 Tree
[r193] by monkeymanstan

Added code to call Picard's SortSam and MarkDuplicates at start of NBP

2013-12-16 16:22:36 Tree
[r192] by tmosbruger

VCFSample: Mark samples with no depth information as no-calls

2013-12-11 18:45:14 Tree
[r191] by biotelerock

DefinedRegionDifferentialSeq
* Changed the default minimum read count threshold to 20 from 10. This lower number was allowing too many low hit genes into the multiple testing correct and causing the FDRs to be significantly lower than necessary.

VCFComparator
* Added checks to convert 0|1 genotypes to 0/1, and 1/0 calls to 0/1; these are needed to standardize the calls and enable genotype matching with the NIST key

SamTranscriptomeParser
* Bug fix for merging paired alignments where an insertion occurred immediately before the start of the second read

2013-12-10 22:50:48 Tree
[r190] by biotelerock

Added modifications to support datasets lacking whole strands, needed for amplicon data.

2013-12-09 22:35:25 Tree
[r189] by biotelerock

Added modifications to support datasets lacking whole strands, needed for amplicon data.

2013-12-09 21:30:22 Tree
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