Mark DePristo c8ed0bfc4c Edge case fixes for BCF2 ... --handle entirely missing GT in a sample in decodeGenotypeAlleles --Create MAX_ALLELES_IN_GENOTYPES constant in BCF2Utils, and extracted its use inline from the code -- Generalized genotype writing code to handle ploidy != 2 and variable ploidy among samples -- Remove special case inline treatment of case where all samples have no GT field values, and moved this into calcVCFGenotypeKeys -- Removed restriction on getPloidy requiring ploidy > 1. It's logically find to return 0 for a no called sample -- getMaxPloidy() in VC that does what it says -- Support for padding / depadding of generic genotype fields		2012-05-24 10:57:06 -04:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.	2012-05-21 15:41:56 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Edge case fixes for BCF2	2012-05-24 10:57:06 -04:00
BaseTest.java	Testing of BCF codec	2012-05-24 10:57:01 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00