Order of header lines messed up

[freeseek]

If I open a VCF file and I immediately write it back to a different file with code like this:
vcf_reader = vcf.Reader(infile)
vcf_writer = vcf.Writer(outfile,vcf_reader)
I get that the order of things in the headers is now messed up. If at first I am more like:

fileformat=VCFv4.1

FORMAT=...

INFO=...

contig=...

reference=...

In the output file things are more like:

contig=...

reference=...

contig=...

fileformat=VCFv4.1

contig=...

INFO=...

FORMAT=...

Is this even allowed by the VCF format? Is there a way to control this behavior?

[martijnvermaat]

This is not allowed by the VCF format (the fileformat header line must be first). Looking at the code, the lines are stored as key/value pairs in a dictionary and retrieved from it in no particular order.

[lennax]

OrderedDict (added in 2.7 I believe)

[jamescasbon]

Fixed in HEAD