Mauricio Carneiro 69b56e11c8 ReadClipper won't modify the original read ... Reverting back to the original implementation, but now including write N's and write Q0's due to walkers that look at the same read multiple times in different reference windows		2012-08-29 11:33:19 -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	ReadClipper won't modify the original read	2012-08-29 11:33:19 -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	One less Queue command line requirement: -tempDir now defaults to .queue/tmp.	2012-08-27 12:04:50 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00