mandawilson/PyVCF — Issue #6: if INFO.Number or FORMAT.Number equal A or G they become None 
Author: mandawilson
Created: 2012-03-05 20:00:51+00:00
State: open

When there is a non-numeric value in INFO.Number or FORMAT.Number it is lost and replaced with None. But VCF 4.1 allows A and G (this is partially done in the code). Also make sure that a "." is read and written correctly (if we want it to be stored as None, make sure it is output as ".").

VCF 4.1:

The Number entry is an Integer that describes the number of values that can be included with the INFO field. For example, if the INFO field contains a single number, then this value should be 1; if the INFO field describes a pair of numbers, then this value should be 2 and so on. If the field has one value per alternate allele then this value should be 'A'; if the field has one value for each possible genotype (more relevant to the FORMAT tags) then this value should be 'G'. If the number of possible values varies, is unknown, or is unbounded, then this value should be '.'. The 'Flag' type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case.