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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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Made all class methods private in the ReadClipper
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2011-12-27 02:11:32 -05:00 |
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codecs
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Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.
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2011-10-27 23:55:11 -04:00 |
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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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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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Fixed NPE in getNextOverlappingBAMScheduleEntry() when mixed mapped/unmapped interval lists are used. Added integrationtest to verify behavior.
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2012-01-12 13:29:11 -05:00 |
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io
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Embedding gsalib source and queueJobReport R scripts in the dist and package jars.
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2011-10-24 15:58:34 -04:00 |
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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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Forgot to test for inter-chromosomal mates in the adaptor clipping
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2011-12-30 00:19:53 -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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Bug fix for incorrect logic in subsetSamples
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2011-12-14 16:14:26 -05:00 |
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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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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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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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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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