Mauricio Carneiro c210b7cde4 Merge GATK repo into CMI-GATK ... Bringing in the following relevant changes: * Fixes the indel realigner N-Way out null pointer exception DEV-10 * Optimizations to ReduceReads that bring the run time to 1/3rd. Conflicts: protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java DEV-10 #resolve #time 2m		2012-10-23 10:59:11 -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
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java	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
keys	…
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	Merge GATK repo into CMI-GATK	2012-10-23 10:59:11 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00