Eric Banks 841a906f21 Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet.		2012-10-20 23:31:56 -04:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
c	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
chainFiles	…
doc	…
java	Adding a hidden (for now) argument to UG (and HC) that tells the caller that the incoming samples are contaminated by N% and to fix it by aggressively down-sampling all alleles. This actually works. Yes, you read that right: given that we know what N is, we can make good calls on bams that have N% contamination. Only hooked up for SNPS right now. No tests added yet.	2012-10-20 23:31:56 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.	2012-10-19 13:20:29 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00