Khalid Shakir 9bee183f6c Switched to using CRAM's SamReader.Indexing implementation. ... CRAM now requires .bai index, just like BAM. Test updates: - Updated existing MD5s, as TLEN has changed. - Tests multiple contigs. - Tests several intervals per contig. - Tests when `.cram.bai` is missing, even when `.cram.crai` is present. Updated gatk docs for CRAM support, including: - Arguments that work for both BAM and CRAM listed as such. - Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM". - Instructions on how to recreate a `.cram.bai` using cramtools. Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.		2015-08-11 17:52:49 -03:00
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src	Switched to using CRAM's SamReader.Indexing implementation.	2015-08-11 17:52:49 -03:00
pom.xml	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00