Skip possible header lines less aggressively in G:M:T:A:Coverage:BamReadcount

There are no tests for these tools.  I have manually run them (specifically `add-readcounts`) on user data that triggered the bug.

The `variant_file` input to BamReadcount was filtering every line as though it could be a header.  This PR makes it consider only the first line in the file.  It was also filtering too aggressively for one user's needs (see support queue).