pezmaster31/bamtools — Issue #29: api read from stdin
Author: earonesty
Created: 2012-01-06 01:51:41+00:00
State: open

I can't seem to get bamtools reader to Open "-" ....

I always get this:

BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for -
Error reading '-': Illegal seek

Code is here:

http://code.google.com/p/ea-utils/source/browse/trunk/clipper/sam-stats.cpp

It hacks around the issue right now by piping to samtools view... which is ugly and slow... it'd like to avoid that.