aaron 7bfb5fad27 fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1676 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-21 23:32:24 +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	Adding the VCF ROD. Also changed the VCF objects to much more user friendly.	2009-09-18 20:19:34 +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	fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test	2009-09-21 23:32:24 +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
MergingIteratorTest.java	General purpose merging iterator implementation	2009-09-12 19:06:15 +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