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annotator
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Update expected test output for Java 7
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2013-05-01 16:18:01 -04:00 |
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beagle
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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bqsr
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Make BQSR calculateIsIndel robust to indel CIGARs are start/end of read
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2013-05-31 13:58:37 -04:00 |
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compression/reducereads
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Fix error in merging code in HC
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2013-05-31 16:29:29 -04:00 |
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diagnostics
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Update MD5s and the Diagnose Target scala script
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2013-05-13 12:06:17 -04:00 |
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diffengine
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Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)
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2013-03-12 10:57:14 -04:00 |
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fasta
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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filters
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Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).
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2013-04-05 00:52:32 -04:00 |
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genotyper
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Bugfix for GGA mode in UG silently ignoring indels
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2013-05-24 13:47:26 -04:00 |
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haplotypecaller
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Break out the GGA kmers and the read kmers into separate functions for the DeBruijn assembler.
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2013-06-03 14:00:35 -04:00 |
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indels
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Secondary alignments were not handled correctly in IndelRealigner
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2013-05-06 19:09:10 -04:00 |
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phasing
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Updated all JAVA file licenses accordingly
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2013-01-10 17:06:41 -05:00 |
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validation
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MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods
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2013-03-29 14:52:10 -04:00 |
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varianteval
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Move some VCF/VariantContext methods back to the GATK based on feedback
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2013-01-29 16:56:55 -05:00 |
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variantrecalibration
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Update MD5s for VQSR header change
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2013-04-16 11:45:45 -04:00 |
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variantutils
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CombineVariants no longer adds PASS to unfiltered records
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2013-05-20 16:53:51 -04:00 |
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