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R
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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baq
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Putative fix for BAQ array out of bounds
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2011-09-21 11:25:08 -04:00 |
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clipping
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Add support for reads starting with insertion
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2012-01-03 09:29:45 -05:00 |
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codecs
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Adding test for reading samtools VCF file
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2012-02-27 17:05:50 -05:00 |
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collections
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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crypt
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Do not fail tests that require the GATK private key if the user does not have permission to read it
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2012-03-06 15:57:02 -05:00 |
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fasta
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Reduced the number of combinations being tested here, which was overkill
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2011-09-01 10:42:43 -04:00 |
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fragments
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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genotype/vcf
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Change interface to getNegLog10PError to getLog10PError
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2011-11-18 21:07:30 -05:00 |
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interval
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make the size of a GenomeLoc int instead of long
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2012-02-03 17:12:42 -05:00 |
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io
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Public-key authorization scheme to restrict use of NO_ET
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2012-03-06 00:09:43 -05:00 |
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pileup
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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report
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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runtime
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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sam
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BQSR with indels integrated!
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2012-02-09 18:46:45 -05:00 |
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text
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GATKReport v0.2:
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2011-08-03 00:24:47 -04:00 |
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threading
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Removed GATK use of distributed parallelism framework.
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2011-07-20 16:26:09 -04:00 |
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variantcontext
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Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.
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2012-03-16 11:14:37 -04:00 |
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BaseUtilsUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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GenomeLocParserUnitTest.java
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During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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2011-11-17 13:56:42 -05:00 |
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GenomeLocSortedSetUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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GenomeLocUnitTest.java
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Support for list of known CNVs in VariantEval
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2011-11-30 17:05:16 -05:00 |
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HaplotypeUnitTest.java
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Adding Unit test for Haplotype class. Used in HC's genotype given alleles mode.
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2012-03-05 21:08:07 -05:00 |
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MWUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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MathUtilsUnitTest.java
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Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly.
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2012-03-05 12:28:32 -05:00 |
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PathUtilsUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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ReservoirDownsamplerUnitTest.java
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Moving reduced read functionality into GATKSAMRecord
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2011-10-21 13:28:05 -04:00 |
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SimpleTimerUnitTest.java
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The right fix for this test is just to delete it.
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2011-11-15 14:53:27 -05:00 |
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UtilsUnitTest.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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