VCF header needs more information

[rmcolq]

All VCFs need the following in their header:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MEAN_FWD_COVG,Number=A,Type=Integer,Description="Mean forward coverage">
##FORMAT=<ID=MEAN_REV_COVG,Number=A,Type=Integer,Description="Mean reverse coverage">
##FORMAT=<ID=MED_FWD_COVG,Number=A,Type=Integer,Description="Med forward coverage">
##FORMAT=<ID=MED_REV_COVG,Number=A,Type=Integer,Description="Med reverse coverage">
##FORMAT=<ID=SUM_FWD_COVG,Number=A,Type=Integer,Description="Sum forward coverage">
##FORMAT=<ID=SUM_REV_COVG,Number=A,Type=Integer,Description="Sum reverse coverage">
##FORMAT=<ID=GAPS,Number=A,Type=Float,Description="Number of gap bases">
##FORMAT=<ID=LIKELIHOOD,Number=A,Type=Float,Description="Likelihood">
##FORMAT=<ID=GT_CONF,Number=1,Type=Float,Description="Genotype confidence">

as well as ##contig=<ID="$id"> for each $id in the CHROM field.

[mbhall88]

In addition. in section 1.4 of the VCF v4.3 specs it says

File meta-information is included after the ## string and must be key=value pairs. Meta-information lines are optional, but if they are present then they must be completely well-formed. Note that BCF, the binary counterpart of VCF, requires that all entries are present. It is recommended to include meta-information lines describing the entries used in the body of the VCF file.

[mbhall88]

We do not output the contig field to the header. This is not required for VCF, but is required for BCF. This is causing problems for me in further analyses