Source Code Log

Commit Date  
[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

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
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
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