David Roazen a96ed385df ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates ... Nasty, nasty bug -- if we were extremely unlucky with shard boundaries, we might end up with a shard containing only unmapped mates of mapped reads. In this case, ReadShard.getReadsSpan() would not behave correctly, since the shard as a whole would be marked "mapped" (since it refers to mapped intervals) yet consist only of unmapped mates of mapped reads located within those intervals.		2012-10-02 13:50:00 -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
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	ReadShard.getReadsSpan(): handle case where shard contains only unmapped mates	2012-10-02 13:50:00 -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	Probably the GATK's most seen typo in the world	2012-10-02 13:34:37 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00