Tablet does not support BAM files with CSI index, only BAI index

[peterjc]

Resurrecting an old issue for the GitHub issue tracker,

The original BAM index format (BAI) has a fixed bin size system, and suffers from a maximum reference sequence length of 512Mbp making it unsuitable for large chromosomes (e.g. many plants, some marsupials).

The newer CSI indexing format supports longer references, and smaller bin sizes - which ought to help with ultra-high coverage in RNA sequencing or viral samples where currently Tablet can struggle and run out of RAM.

Testing with samtools 1.3, e.g. samtools index -c -m 5 example.bam, gives an index file example.bam.csi but Tablet does not recognise this.

Needs support in htslib samtools/htsjdk#447

The htslib issue is still open, so I assume that has not yet been implemented.

[peterjc]

Htsjdk supports reading CSI indexes as of 2.19.0