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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo e9c22b9aad Final updates to integration tests for BCF2 
-- Fully working version
-- Use -generateShadowBCF to write out foo.bcf as well as foo.vcf anywhere you use -o foo.vcf
-- Moved MedianUnitTest to its proper home in Utils
-- Added reportng to ivy and testng, so build/report/X/html/ is a nicely formatted output for Unit and Integration tests.  From this website it's easy to see md5 diffs, etc.  This is a vastly better way to manage unit and integration test output
 		2012-05-24 10:58:59 -04:00
..
R Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
activeregion Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
clipping Add support for reads starting with insertion 2012-01-03 09:29:45 -05:00
codecs Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
crypt Do not fail tests that require the GATK private key if the user does not have permission to read it 2012-03-06 15:57:02 -05:00
fasta Reduced the number of combinations being tested here, which was overkill 2011-09-01 10:42:43 -04:00
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
genotype/vcf GATK now writes BCF output to any file with .bcf extension 2012-05-24 10:57:00 -04:00
interval GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
io Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
recalibration disabling all BQSR unit tests 2012-04-30 14:39:55 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped 2012-04-27 09:58:38 -04:00
text Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Renamed NO_HEADER to the more accurate no_cmdline_in_header 2012-05-24 10:57:08 -04:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
BitSetUtilsUnitTest.java BitSets keys to lower BQSR's memory footprint 2012-03-16 13:01:48 -04:00
GenomeLocParserUnitTest.java During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. 2011-11-17 13:56:42 -05:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Support for list of known CNVs in VariantEval 2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned. 2012-04-04 16:04:29 -04:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java minor misc optimizations to PairHMM 2012-04-18 15:02:26 -04:00
MedianUnitTest.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
PairHMMUnitTest.java Resolve merge conflicts 2012-04-18 16:25:03 -04:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QualityUtilsUnitTest.java Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. 2012-03-21 08:45:42 -04:00
ReservoirDownsamplerUnitTest.java Moving reduced read functionality into GATKSAMRecord 2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java The right fix for this test is just to delete it. 2011-11-15 14:53:27 -05:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00