[BQ to VCF] order INFO fields as they are listed in the header

[mbookman]

This does not appear to be a requirement from the VCF spec, but may be worthwhile to at least follow as a convention.

Looking at the output of a joint genotype file from the Broad institute, the INFO field keys are sorted alphabetically in the header and in the actual values. For example:

the first few ##INFO directives from the header:

##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
...

and an example value:

AC=4;AF=4.630e-03;AN=864;DP=2456;ExcessHet=0.0001;FS=0.000;InbreedingCoeff=0.0339;MLEAC=11;MLEAF=0.013;MQ=36.12;QD=27.40;SOR=4.977;VQSLOD=-5.582e+01;culprit=SOR;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV||||||||||||||||||||||||||||||||||||||||||

I ran an export using bq_to_vcf which passed the original header as a representative header file and the same INFO field value looks like:

MLEAC=11;AC=4;FS=0.0;MLEAF=0.013;InbreedingCoeff=0.0339;culprit=SOR;ExcessHet=0.0001;VQSLOD=-55.82;AF=0.00463;AN=864;SOR=4.977;MQ=36.12;QD=27.4;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||SNV||||||||||||||||||||||||||||||||||||||||||;DP=2456

There are a few small differences in numeric formatting (but otherwise values are the same).
The INFO field ordering appears arbitrary.