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Eric Banks 12fc198b80 Added better error message for BAMs with bad read groups. 
* Split the cases into reads that don't have a RG at all vs. those with a RG that's not defined in the header.
  * Added integration tests to make sure that the correct error is thrown.
  * Resolved GSA-407.
 		2013-02-27 16:02:56 -05:00
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R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc
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java Added better error message for BAMs with bad read groups. 2013-02-27 16:02:56 -05:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages ValidatingPileup was renamed to CheckPileup 2013-02-15 11:56:19 -05:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest 2013-02-27 04:45:53 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00