ebanks 44f3c5639a I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such... ... We can now emit bzipped VCFs from the GATK. Details: any walker that defines a VCFWriter for its @Output (i.e. pretty much every core walker from UG and on), also has associated with it the -bzip (--bzip_compression) boolean argument. When set, it will emit a VCF that is compressed with bzip2. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4093 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-24 04:14:50 +00:00
..
arguments	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
contexts	Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.	2010-08-16 13:46:22 +00:00
datasources	Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.	2010-08-16 13:46:22 +00:00
examples	Add deprecated command-line arguments, and switched over UG to output to	2010-08-22 21:01:44 +00:00
executive	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
filters	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
io	I have finally figured out that when you volunteer to do something in group meeting, you keep getting pestered about it on Mark's Omniplan doc until it gets done (except for contig aliasing, of course). As such...	2010-08-24 04:14:50 +00:00
iterators	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
refdata	adding the ability in Tribble to create indexes from a stream of features, so that we can create multiple indexes from one pass of the file. In the GATK we now create multiple indexes, and choose the	2010-08-23 06:54:59 +00:00
traversals	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
walkers	Force isRequired() to be false for @Deprecated args.	2010-08-23 23:50:30 +00:00
CommandLineExecutable.java	allow other objects access to the static method that resolves bam lists, and some renaming and improved documentation for the function.	2010-08-23 18:52:00 +00:00
CommandLineGATK.java	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
DownsampleType.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
DownsamplingMethod.java	We're unable to make the naive deduper more worldly, so we're killing it instead.	2010-06-18 13:54:27 +00:00
GATKErrorReport.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
GenomeAnalysisEngine.java	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
ReadMetrics.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
ReadProperties.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
WalkerManager.java	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00