jamescasbon/PyVCF — pull request #143 by datagram (2014-02-06 09:34:47+00:00)
Title: Fix for issue #140, add vcf_record_sort_key arg

- Added 'vcf_record_sort_key' when allows users to specify any chromosome ordering.
- Fixed issue #140 by emit all records from the current chromosome before moving on to the next one. This takes care of the problem in the typical case (when all files have records for all contigs), but still fails in some edge cases (when vcf files have differing sets of contigs and where the alphabetical order of these contigs is not the desired order). In those edge cases, the 'vcf_record_sort_key' arg can be used to fully solve the problem by explicitly defining the chromosome order.