Johan Dahlberg e9b9e2318c Fixed SortSam bug, for .done file ... The *.bai.done file for the .bai file was written in the run directory instead of in the specified output directory. Changing getName() to getAbsolutePath() fixes this. Signed-off-by: Joel Thibault <thibault@broadinstitute.org>		2012-10-09 16:25:18 -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
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doc	…
java	Fixing merge conflicts related to the comment formatting in the BQSR.	2012-10-08 10:23:08 -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	Fixed SortSam bug, for .done file	2012-10-09 16:25:18 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00