samtools/bcftools — pull request #23 by sm15 (2014-02-05 09:21:35+00:00)
Title: further updates to bcftools view options

* replace `--biallelic`/`--multialleic` options with more general `--min-alleles`/`--max-alleles`

* drop the `--exclude-ref` option as it is covered by `-c1` option; test updated to reflect this

* optionally specify that `--min-ac` and/or `--max-ac` are referring to the non-ref alleles (default), minor allele or first alternate allele

* add options `--min-af` and `--max-af` similar to `--min-ac` and `--max-ac`

* fix typo in `--known`/`--novel` description

* long option `--include-types` changed to `--types` for consistency

* new option `--uncalled` to complement `--exclude-uncalled`

* add tests for new options and a lot of the existing options

* `--singleton` and `--doubleton` options dropped as their current functionality covered by `--max-ac`. Could reintroduce something better later.