Guillermo del Angel 27b1aa5dd3 Don't allow N's in insertions when discovering indels. Maybe better solution will be to use them as wildcards and merge them with compatible regular insertion alleles but for now it's easier to ignore them. Minor refactoring of Allele.accepableAlleleBases to support this. Added unit test to test consensus allele counter in presence of N's		2012-05-10 10:29:19 -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	Don't allow N's in insertions when discovering indels. Maybe better solution will be to use them as wildcards and merge them with compatible regular insertion alleles but for now it's easier to ignore them. Minor refactoring of Allele.accepableAlleleBases to support this. Added unit test to test consensus allele counter in presence of N's	2012-05-10 10:29:19 -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	Nope, loads of integration tests had to be changed.	2012-05-07 14:30:42 -04:00
BaseTest.java	Don't allow N's in insertions when discovering indels. Maybe better solution will be to use them as wildcards and merge them with compatible regular insertion alleles but for now it's easier to ignore them. Minor refactoring of Allele.accepableAlleleBases to support this. Added unit test to test consensus allele counter in presence of N's	2012-05-10 10:29:19 -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