Running somalier on bam files in s3?

[nspies-celsiustx]

This is a great tool -- thanks for developing and sharing with the community. Using the precompiled binaries for somalier I'm not able to read directly from s3. I've verified I can samtools view the file directly from s3. The error I get is

Error: unhandled exception: unable to open file:s3://path-to-my-files-here [OSError]

Since somalier is so fast, downloading the files is the bottleneck. It looks like hts-nim should be able to read from s3. Can you give an outline of how to run somalier on s3 files (eg how to recompile with s3 support)?

[brentp]

hi, there may be a regression in how I build the binary such that S3 is not supported. I will look into it for next release. Thanks for reporting.
Just to be sure, you can run samtools view on a bam file for which you see this error.

[nspies-celsiustx]

Just to be sure, you can run samtools view on a bam file for which you see this error.

Thanks for the quick response! Yes, I can samtools view s3://path-to-my-file-here.bam | less but get the above error from somalier.

[cfrech-ctx]

@brentp - has there been an update on this? I just tried with the latest version and still see the above error.