Khalid Shakir c3c7f17d90 Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. ... Instead of creating a supposed network temporary directory locally which then fails when remote nodes try to access the non-existant dir, now checking to see if they network directory is available and throwing a SkipException to bypass the test when it cannot be run. TODO: Throw similar SkipExceptions when fastas are not available. Right now instead of skipping the test or failing fast the REQUIRE_NETWORK_CONNECTION=false means that the errors popup later when the networked fastas aren't found.		2012-05-29 11:18:22 -04:00
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alignment	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
analyzecovariates	Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.	2012-02-03 17:13:52 -05:00
commandline	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
gatk	DiagnoseTargets with working Q1,Median,Q3	2012-05-29 10:16:45 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -04:00
utils	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00