Mark DePristo 8cdeb51b78 Cleanup printProgress in TraversalEngine ... -- Separate updating cumulative traversal metrics from printing progress. There's now an updateCumulativeMetrics function and a printProgress() that only takes a current position -- printProgress now soles relies on the time since the last progress to decide if it will print or not. No longer uses the number of cycles, since this isn't reliable in the case of nano scheduling -- GenomeAnalysisEngine now maintains a pointer to the master cumulative metrics. getCumulativeMetrics never returns null, which was handled in some parts of the code but not others. -- Update all of the traversals to use the new updateCumulativeMetrics, printProgress model -- Added progress callback to nano scheduler. Every bufferSize elements this callback is invoked, allowing us to smoothly update the progress meter in the NanoScheduler -- Rename MapFunction to NanoSchedulerMap and the same for reduce.		2012-09-05 15:45:23 -04:00
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commandline	- New UserExceptions added for when ReadFilters or Walkers specified on the command line are not found. When -rf xxxx cannot find the class corresponding to xxxx, all read filters are printed in a better formatted way, with links to their gatk docs.	2012-09-04 16:41:44 -04:00
gatk	Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig	2012-09-05 15:45:22 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Cleanup printProgress in TraversalEngine	2012-09-05 15:45:23 -04:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	On the way to really sorting out HMS error handling	2012-07-25 22:11:10 -04:00