Mark DePristo 9bf1d138d9 New GATK argument interface for data and cpu threads ... -- Closes GSA-515 Nanoscheduler GSA-542 Good interface to nanoScheduler -- Old -nt means dataThreads -- New -cnt (--num_cpu_threads_per_data_thread) gives you n cpu threads for each data thread in the system -- Cleanup logic for handling data and cpu threading in HMS, LMS, and MS -- GATKRunReport reports the total number of threads in use by the GATK, not just the nt value -- Removed the io,cpu tags for nt. Stupid system if you ask me. Cleaned up the GenomeAnalysisEngine and ThreadAllocation handling to be totally straightforward now		2012-09-05 15:45:24 -04:00
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R	Actually load the library necessary to compactPDF	2012-08-28 08:06:47 -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	New GATK argument interface for data and cpu threads	2012-09-05 15:45:24 -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	Update from dbsnp135 to dbsnp137.	2012-08-31 14:06:29 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00