Eric Banks 66cbaaee31 Fixed nasty bug in BQSR csv file creation: ... numbers larger than 999 in the Errors column were printed out with commas (which looks like a separate column). This wasn't caught earlier because there are no integration tests covering the csv. I'll add one into unstable in a sec.		2012-11-09 08:33:55 -05:00
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covariates	Thread-safe ReadGroupCovariate	2012-10-24 15:22:50 -04:00
BQSRMode.java	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
BQSRReadTransformer.java	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
BaseRecalibration.java	BaseRecalibration: don't cache instances of ReadCovariates across reads	2012-10-25 17:02:55 -04:00
EventType.java	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
QualQuantizer.java	Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.	2012-08-08 14:34:16 -04:00
QuantizationInfo.java	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
ReadCovariates.java	Make BaseRecalibration thread-safe	2012-08-31 13:42:42 -04:00
RecalDatum.java	Fixed nasty bug in BQSR csv file creation:	2012-11-09 08:33:55 -05:00
RecalDatumNode.java	Initial commit of the delocalized BQSR written as a read walker.	2012-08-28 15:24:20 -04:00
RecalUtils.java	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
RecalibrationReport.java	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -04:00
RecalibrationTables.java	BQSR: allow logging recal table updates to a file	2012-10-01 14:18:34 -04:00