9bee183f6c
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()`. |
||
|---|---|---|
| .. | ||
| main | ||
| test | ||