ebanks 65edbced36 Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4227 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-08 04:02:14 +00:00
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alignment	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
analyzecovariates	Committing Michael Yourshaw's patch for AnalyzeCovariates. We spawn each RScript process and wait for it to finish in series. Thanks Michael!	2010-08-24 13:06:25 +00:00
commandline	Improved interface to getting command line options. Now fully traverses all objects to get all internal argument collections. Preliminary (but disabled version) of phoning home (see -et argument for more information). Captures correct and erroring out runs and writes out gzipped, xml report with lots of useful information. Needs a bit more information but is approximately working. Reports going to /humgen/gsa-hpprojects/GATK/reports/ in submitted directory that will be collated by some external tool. Only operating if -et STANDARD or -et STDOUT are provided currently and REPORT_DIR contains a file called ENABLE. WalkerTest now adds -et NO_ET to tests to avoid populating the reports with tests.	2010-08-28 22:53:32 +00:00
gatk	Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information.	2010-09-08 04:02:14 +00:00
oneoffprojects	Minor improvements to indel genotyper:	2010-09-03 22:52:08 +00:00
playground	QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG	2010-09-03 18:21:43 +00:00
queue	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
utils	QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG	2010-09-03 18:21:43 +00:00