41ffd08d53
On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live.
2012-02-13 12:35:09 -05:00
894d3340be
Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
2012-02-03 17:13:52 -05:00
6592972f82
Putative fix for BAQ array out of bounds
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-- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
2011-09-21 11:25:08 -04:00
ecc7f34774
Putative fix for BAQ problem.
2011-09-21 11:09:54 -04:00
9992c373be
Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.
2011-07-17 20:29:58 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Ryan Poplin
Mark DePristo
David Roazen