Support for BAM CSI index

genome / bam-readcount

Count bases in BAM/CRAM files

MIT License

298 stars 95 forks source link

Support for BAM CSI index #89

Closed f-huber closed 2 years ago

f-huber commented 2 years ago

bam-readcount does not handle csi format.

Although .csi files are in the directory, bam-readcount reports:

Minimum mapping quality is set to 1 Expect library: samplename in BAM [bam_index_load] fail to load BAM index. BAM indexing file is not available.

Is .csi format expected to be supported in the future? This might be useful since this indexing format has a higher limit for the size of individual chromosomes.

Thank you very much for your work

f-huber commented 2 years ago

Sorry, I was accidently working with an old version of bam-readcount. csi format is supported in bam-readcount v1.0.0