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gatk-3.8/java/test/org/broadinstitute/sting/utils
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aaron 8ee5c7de8e GLF reader and writer check in. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1202 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-07-08 23:06:37 +00:00
..
cmdLine Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing. 2009-07-08 20:26:16 +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 GLF reader and writer check in. 2009-07-08 23:06:37 +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 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
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
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