ftp and http access?

[Hypercubed]

I don't see anywhere in the documentation that ftp and http file locations are supported however the following command works fine:

bamtools count -in ftp://encodeftp.cse.ucsc.edu/pipeline/hg19/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqK562R1x75dAlignsRep2V2.bam -region chr8:128746973-128755020
90772

But the following doesn't:

bamtools count -in http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/wgEncodeCaltechRnaSeqGm12878R1x75dSplicesRep1V2.bam -region chr8:128746973-128755020

I'm using cygwin under window 7.

Is HTTP access not yet fully functional? Thank you for your help (and the great tool).

[pezmaster31]

FTP & HTTP support are both available, I just haven't made a big announcement or documented yet - precisely for reasons like this. It works most of the time just fine, but there's still the occasional quirk that keeps me from fully feeling comfortable with publicizing it. These issues are typically tricky to reproduce, related to network traffic, I/O wait, etc. Sometimes trying the same command a few seconds later works just fine; kinda frustrating from a developer's perspective.

In any case, improving the remote I/O stability is a major item on my roadmap for the next major release (BamTools 3.0). Thanks for the feedback and compliments.

Just curious - what's the output from the failed count command? Is it an actual, explicit "error" message or just a count of zero?

[Hypercubed]

No output at all when trying to access over http. Just idles for hours.