Hi,

I cannot find any indication that CSI indexes are supported by Rsamtools and I cannot access a BAM file indexed with a CSI index. I indexed it with samtools index -c my.file.bam and on the command line samtools idxstats my.file.bam worked correctly, so the index is correct.

However, when I create the BamFile object with Rsamtools::BamFile(file = "my.file.bam") it does not find the index

class: BamFile 
path: my.file.bam
index: NA
isOpen: FALSE 
yieldSize: NA 
obeyQname: FALSE 
asMates: FALSE 
qnamePrefixEnd: NA 
qnameSuffixStart: NA

and trying to access it with Rsamtools::idxstatsBam(file = MyBamFile) fail with error Error in Rsamtools::idxstatsBam(file = data) : file.exists(index(file)) is not TRUE.

Am I missing something? or CSI indexes are not supported? If so, are there any plans to support them?

Thanks!

Bernat

The index file can be specified explicitly as a second argument to BamFile(). But it might be that the CSI index does not work; you might try (on a non-Windows, and this would be an advanced / unsupported step) installing the in-development versions

BiocManager::install("Bioconductor/Rhtslib", ref = "enable-cram")
BiocManager::install("Bioconductor/Rsamtools", ref = "cram")

It would be useful to me to know how this goes...