Changes

   As BCF is a restrictive format of VCF where all meta data must be present in the header,  

   As BCF is a restrictive format of VCF where all meta data must be present in the header,  

   vt provides a mechanism to read an alternative header for VCF files that do not have a  

   vt provides a mechanism to read an alternative header for VCF files that do not have a  

   complete header.  Simply provide a header file stub named as <vcf-file>.hdr and vt

   well formed header.  Simply provide a header file stub named as <vcf-file>.hdr and vt

   will automatically read it instead of the original header in <vcf-file>.

   will automatically read it instead of the original header in <vcf-file>.

   This mechanism is very safe to use if one is reading VCF or compressed VCF files.

   This mechanism is safe to use if one is reading VCF or compressed VCF files.

   However it is not meant for BCF files as the assumption for BCF files is that the

   However it is not meant for BCF files as the assumption for BCF files is that the

   header is already well formed.

   header is already well formed.  This might corrupt the BCF file reading as the encoding

  of the fields in BCF records are based on the order of the meta info lines in the header.

== General cases of Ploidy and Alleles ==

== General cases of Ploidy and Alleles ==