aaron 09811b9f34 Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-11 19:51:05 +00:00
..
bed	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
cmdLine	Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.	2009-09-29 22:23:19 +00:00
fasta	A bit of cleanup in preparation for Picard patch.	2009-12-08 16:09:04 +00:00
genotype	Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well.	2009-12-11 19:51:05 +00:00
sam	changes to fix and test the interval based traversals	2009-06-25 17:54:15 +00:00
threading	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
BaseUtilsTest.java	Added tests for mostFrequentBaseFraction() and reverseComplementString()	2009-06-09 00:53:45 +00:00
ExpandingArrayListTest.java	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +00:00
GenomeLocParserTest.java	fixed a bug I checked in that Eric found, for intervals with no start or stop coordinate. Now I owe Eric a cookie, and Milk Street is so far away. Damn.	2009-09-22 04:34:18 +00:00
GenomeLocSortedSetTest.java	a couple of light changes to GenomeLocSortedSet.	2009-09-23 20:38:53 +00:00
GenomeLocTest.java	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
GenotypeUtilsTest.java	Removing the AllelicVariant interface, which is replaced by the Variation interface.	2009-10-06 17:44:24 +00:00
ListUtilsTest.java	Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.	2009-09-28 18:12:32 +00:00
MathUtilsTest.java	A more thorough test for multinomialProbability.	2009-05-01 06:27:05 +00:00
MergingIteratorTest.java	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +00:00
PathUtilsTest.java	Test class for PathUtils.	2009-05-21 19:31:22 +00:00
UtilsTest.java	a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.	2009-11-17 16:50:01 +00:00