Support both HDFS and NFS/other file systems for BAM files

[jaclynperrone]

for uploaded BAM files

[hammer]

Cf. #682 #663

[hammer]

I think it makes sense to support object stores (e.g. S3) as well for BAM/VCF storage.

[ckandoth]

I'm testing out Cycledash as a way to compare test/truth VCFs, and to easily view discordant calls in IGV. Since our BAMs are not in HDFS, this issue seems to be the only bottleneck. Please advise on a workaround, if any. Thanks! And really nice work, so far.

[ihodes]

Thanks for checking out Cycledash, Cyriac! I'm looking into what's required on Cycledash's end to support this, and it looks like a relatively simple change that I hope to get to soon. On your side of things, the BAMs would need to be accessible via HTTP (using any old server that supports HTTP range requests—most HTTP servers barring Python's SimpleHTTPServer). Please let me know how else I can help, and I'll let you know when this feature is added.

[hammer]

@ckandoth also you can sign up for our public Slack instance where we hope to support users of our software, some day: http://publicslack.hammerlab.org.

[ihodes]

Hi Cyriac; this should be fixed on #865 (not yet merged into master), so please feel free to give it a whirl if you'd like.