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annotator
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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concordance
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Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.
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2009-12-29 17:30:47 +00:00 |
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fasta
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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filters
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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genotyper
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Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful.
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2009-12-29 17:30:47 +00:00 |
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indels
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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recalibration
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Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now.
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2009-12-29 21:01:32 +00:00 |
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DepthOfCoverageIntegrationTest.java
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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PileupWalkerIntegrationTest.java
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moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest.
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2009-12-29 07:40:48 +00:00 |
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PrintReadsWalkerTest.java
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A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).
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2009-10-02 19:35:35 +00:00 |
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