broadinstitute/gamgee — pull request #357 by droazen (2014-11-06 21:51:25+00:00)
Title: Update gamgee to work with revved version of htslib

We just updated our htslib fork with the last 3 months' worth of changes
from upstream. A few things in gamgee broke as a result and needed to be
fixed:

-Updated a few htslib API calls in gamgee whose names had changed in upstream

-Sync variant headers in VariantHeaderBuilder when building headers

htslib no longer calls bcf_hdr_sync() for us each time we modify
a variant header, so we need to call it ourselves in VariantHeaderBuilder
at build time

-Sync variant headers when merging multiple headers

Another consequence of htslib's new, lazier approach to variant
header synchronization: we need to explicitly call bcf_hdr_sync()
when merging variant headers