samtools/htslib — pull request #10 by jrandall (2013-04-02 21:10:17+00:00)
Title: Fix for fileversion header not coming first in VCF output (e.g. from vcfview)

A recent change has made the FILTER line defining the PASS filter come as the first line in the VCF/BCF output, which appears to be against both the VCF and BCF specs. I've patched it so that before the hardcoded PASS filter there is now also a hardcoded fileformat header (for VCF 4.1), and in the header passthrough loop skipping the processing of the existing fileformat header. An alternative would be to move the PASS filter output into the loop so that it follows whatever fileformat line is already present, but I thought that htslib is probably only going to be outputting the latest VCF version.