David Roazen 2a7af43164 Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest ... -Some QScripts used by public pipeline tests unnecessarily used the (now protected) UnifiedGenotyper. Changed them to use PrintReads instead. -Moved ExampleUnifiedGenotyperPipelineTest to protected -Attempt to fix the flawed and sporadically failing MisencodedBaseQualityUnitTest: After looking at this class a bit, I think the problem was the use of global arrays for the quals shared across all reads in all tests (BAMRecord class definitely does not make a separate copy for each read!). One test (testFixBadQuals) modifies the bad quals array, and if this happens to run before the testBadQualsThrowsError test the bad quals array will have been "fixed" and no exception will be thrown.		2013-02-27 04:45:53 -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	…
doc	…
java	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -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