depristo 3e3ec85807 Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5433 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-13 15:24:22 +00:00
..
arguments	Add hidden command-line argument for low-memory sharding.	2011-03-02 15:13:16 +00:00
contexts	CalculateChromosomeCounts() now only calculates AC, AF, and AN when there are genotypes. Can now combine variants with headers that differ in only whether a field is a integer or a float. Updated CombineVariants integrationtest, as incorrect AC values where being calculated in the previous GS outputs.	2011-03-06 19:25:52 +00:00
datasources	A few quick fixes to temporarily make the LowMemorySharder return exactly the	2011-03-07 22:43:14 +00:00
examples	Fare thee well, UGv1. Here come the days UGv2.	2010-11-29 21:51:19 +00:00
executive	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
filters	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00
io	New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so.	2011-03-10 02:48:29 +00:00
iterators	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00
phonehome	Cleaner error (really now just warnings) if you can't reach the S3 for logging	2011-03-05 06:08:35 +00:00
refdata	Miscellaneous changes:	2011-03-03 22:43:36 +00:00
report	Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R.	2011-02-17 23:03:46 +00:00
traversals	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
walkers	Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats.	2011-03-13 15:24:22 +00:00
CommandLineExecutable.java	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
CommandLineGATK.java	Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here.	2010-10-22 15:22:17 +00:00
DownsampleType.java	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
DownsamplingMethod.java	Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.	2010-09-12 14:02:43 +00:00
GenomeAnalysisEngine.java	Add hidden command-line argument for low-memory sharding.	2011-03-02 15:13:16 +00:00
ReadMetrics.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
ReadProperties.java	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
WalkerManager.java	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +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