Mark DePristo 6382d5bdc9 Final cleanup and unit testing for GATKRunReport ... -- Bringing code up to document, style, and code coverage specs -- Move GATKRunReportUnitTest to private -- Fully expand GATKRunReportUnitTests to coverage writing and reading GATKRunReport to local disk, to standard out, to AWS. -- Move documentation URL from GATKRunReport to UserException -- Delete a few unused files from s3GATKReport -- Added capabilities to GATKRunReport to make testing easier -- Added capabilities to deserialize GATKRunReports from an InputStream		2013-02-02 15:06:56 -05:00
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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	Final cleanup and unit testing for GATKRunReport	2013-02-02 15:06:56 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Rev picard, sam-jdk, and tribble	2013-02-01 13:51:30 -05:00
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	Making metrics a required parameter in MarkDuplicates	2013-01-25 17:49:49 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00