fix reading VCF with no header

[ClayBirkett]

When the VCF has no header then the first few accessions are skipped while loading This modification works on the transposed file

5203

Checklist

• [ ] Refactoring only
• [ ] Documentation only
• [ ] Fixture update only
• [x ] Bug fix
  • [ ] The relevant issue has been closed.
  • [ ] Further work is required.
• [ ] New feature
  • [ ] Relevant tests have been created and run.
  • [ ] Data was added to the fixture
  • [ ] Data was added via a patch in /t/data/fixture/patches/.
  • [ ] User-Facing Change
  • [ ] The user manual in /docs has been updated.
  • [ ] Any new Perl has been documented using perldoc.
  • [ ] Any new JavaScript has been documented using JSDoc.
  • [ ] Any new legacy JavaScript has been moved from /js to /js/source/legacy.

[lukasmueller]

Instead of starting with the first line that contains number - slash - number, the parsing should simply start at the line after the line starting with #CHROM ?

[ClayBirkett]

The error is when reading in the transposed VCF so there is no #CHROM line. It might be that the problem is with the creation of the transposed file not reading the file.

[lukasmueller]

In the code it actually skips 8 entries, which is correct for the untransposed file, but probably incorrect for the transposed file?

[ClayBirkett]

I have it working now. The problem was that the parse_with_plugin() function was reading a fixed number of comment lines which is never true. I changed this to read all lines starting with "##", the comment lines. Then the next_genotype() function then skips the crhom, pos, id, ref, alt correctly