Eric Banks b6839b3049 Added checking in the GATK for mis-encoded quality scores. ... The check is performed by a Read Transformer that samples (currently set to once every 1000 reads so that we don't hurt overall GATK performance) from the input reads and checks to make sure that none of the base quals is too high (> Q60). If we encounter such a base then we fail with a User Error. * Can be over-ridden with --allow_potentially_misencoded_quality_scores. * Also, the user can choose to fix his quals on the fly (presumably using PrintReads to write out a fixed bam) with the --fix_misencoded_quality_scores argument. Added unit tests.		2012-12-03 11:18:41 -05:00
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AlignmentUtilsUnitTest.java	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
ArtificialPatternedSAMIteratorUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMFileWriterUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMQueryIteratorUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSingleSampleReadStreamUnitTest.java	Downsampling: experimental engine integration	2012-09-06 15:03:27 -04:00
GATKSAMRecordUnitTest.java	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -04:00
MisencodedBaseQualityUnitTest.java	Added checking in the GATK for mis-encoded quality scores.	2012-12-03 11:18:41 -05:00
ReadUtilsUnitTest.java	Unit tests for GATKSAMRecord class	2012-01-26 17:06:36 -05:00