Lechu 027843d791 I've simply added a "library(grid)" call at the beginning of the R script generation since R 2.14.2 doesn't seem to load the "grid" package as default. I haven't tested it on previous R versions (you may edit the R version comment to be more precise if desired), but I'm almost certain that this library call shouldn't do any harm on them. ... Signed-off-by: Ryan Poplin <rpoplin@broadinstitute.org>		2012-03-05 21:27:03 -05:00
..
arguments	Document -L unmapped	2012-02-07 13:30:54 -05:00
contexts	Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.	2011-11-05 23:54:28 -04:00
datasources	Merged bug fix from Stable into Unstable	2012-02-27 17:13:17 -05:00
examples	@Hidden for DocumentationTest and GATKDocsExample	2011-09-23 09:03:37 -04:00
executive	Documentation request by Eric. At each stage of the GATK where filtering occurs, added documentation suggesting the goal of the filtering along with examples of suggested inputs and outputs.	2012-02-09 11:24:52 -05:00
filters	It wouldn't harm integrationtests if we had our logic right... :-)	2011-11-10 14:03:22 -05:00
io	Fixed long-standing bug in tribble index creation	2011-09-20 10:53:18 -04:00
iterators	Merged bug fix from Stable into Unstable	2012-02-27 17:13:17 -05:00
phonehome	S3 upload now directly creates the XML report in memory and puts that in S3	2012-01-29 15:14:58 -05:00
refdata	Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.	2011-11-28 14:18:28 -05:00
report	Revert "First implementation of GATKReportGatherer"	2012-02-08 23:28:55 -05:00
resourcemanagement	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
samples	Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.	2011-12-09 14:51:34 +01:00
traversals	Adding Genotype Given Alleles mode to the HaplotypeCaller. It constructs the possible haplotypes via assembly and then injects the desired allele to be genotyped.	2012-02-18 10:31:26 -05:00
walkers	I've simply added a "library(grid)" call at the beginning of the R script generation since R 2.14.2 doesn't seem to load the "grid" package as default. I haven't tested it on previous R versions (you may edit the R version comment to be more precise if desired), but I'm almost certain that this library call shouldn't do any harm on them.	2012-03-05 21:27:03 -05:00
CommandLineExecutable.java	Removed -B support. Now explodes with error if -B provided.	2011-08-16 16:13:47 -04:00
CommandLineGATK.java	Weirdly, PicardException inherits from SAMException, which means that our specialty code for	2012-01-24 15:30:04 -05:00
DownsampleType.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
DownsamplingMethod.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeAnalysisEngine.java	On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.	2012-02-13 12:35:09 -05:00
ReadMetrics.java	Counts of records failing filters are displayed sorted	2011-10-06 18:42:26 -07:00
ReadProperties.java	On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.	2012-02-13 12:35:09 -05:00
WalkerManager.java	Removed support for RMD in @Requires and @Allows	2011-08-03 15:36:55 -04:00
package-info.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00