Creating a bai index from a CRAM file

[BeatWolf]

Hi, i need to be able to quickly tell how many reads are mapped on the different sequences in an alignment. the crai index does not seem to support this, which means i need a bai index.

Now, i'm using :
CRAMBAIIndexer.createIndex(new SeekableFileStream(file), indexFile, logger, ValidationStringency.STRICT);

But this does not seem to work. The bai file contains now read counts (mapped, unmapped etc.). Looking at the code, that makes sense, as it is using the codepath that is explicitely not decoding the individual records.
When looking at the samtools code, it seems like there is a reasonably fast way to count the reads without having to fully decode them:
https://github.com/samtools/samtools/blob/147ac2f83857d6209e344a77a2ae74324975fc67/bam_index.c#L160

So my question is, is there a way with htsjdk to create the bai index, or otherwise count the reads without having the decode the full CRAM file with the reference etc.?