aaron 6313c465fb we want the RMS of the reads qualities not the RMS of the RMS of the read qualities. ... Also the VCF version tag seems to be standardized as VCR. Updated the VCF code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1447 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-20 21:56:29 +00:00
..
cmdLine	Cleaning up, preparing to incorporate a better fix for Eric's problems with validation stringency in BAM files opened directly from the walkers.	2009-07-13 01:42:13 +00:00
fasta	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
genotype	we want the RMS of the reads qualities not the RMS of the RMS of the read qualities.	2009-08-20 21:56:29 +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 version of the recalibration tool	2009-06-19 17:45:47 +00:00
GenomeLocParserTest.java	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
GenomeLocSortedSetTest.java	added a big speed-up for interval list input processing. With large interval sets this was taking way too long...	2009-07-13 22:00:00 +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
ListUtilsTest.java	Tests for downsampling related utilities in ListUtils class that didn't get checked in earlier	2009-07-31 00:09:35 +00:00
MathUtilsTest.java	A more thorough test for multinomialProbability.	2009-05-01 06:27:05 +00:00
PathUtilsTest.java	Test class for PathUtils.	2009-05-21 19:31:22 +00:00
RefHangerTest.java	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
UtilsTest.java	other fixes for some broken unit tests	2009-07-07 05:53:13 +00:00