making alternate allele frequency work in the case of non-diploid alleles
fixing small typo in elif in test case for aaf
adding one more test case for non-diploids
updating ploidy vcf example file
Use requirements files to consolidate dependencies.
Merge pull request #159 from gotgenes/feature-use_requirements_files

Use requirements files to consolidate dependencies.
Adds _Record.affected_start and .affected_end.

These coordinates should represent the zero-based, half-open region of
the reference sequence affected by all the events included in ALT. These
coordinates allow the user to identify precisely which bases are altered
by the events in the record.

Provides more thorough documentation on the coordinate schemes for
_Record.POS, .start, and .end.
Merge pull request #161 from gotgenes/feature-affected_coordinates

Adds _Record.affected_start and .affected_end.
Merge pull request #148 from mgymrek/master

making alternate allele frequency work in the case of non-diploid genotypes
Allow flag INFO field to be declared as string

As reported in #164, we previously crashed on flag INFO fields declared
as strings (and the number of values declared as 1). This is indeed not
according to spec, but we should probably allow it anyway.
Don't crash when FORMAT is set to the missing value (.)

It is not valid according to the spec, but issue #164 shows a VCF file
where the FORMAT column contains just a dot character. We have no way
of interpreting the subsequent genotype columns in that case, so this
patch ignores them.
Merge pull request #165 from martijnvermaat/string_as_flag

Allow flag INFO field to be declared as string
Merge pull request #166 from martijnvermaat/format-none

Don't crash when FORMAT is set to the missing value (.)
Don't crash on metadata lines without value

The spec actually does not allow for metadata lines without value, but we
shouldn't crash on them.

Fixes #168
Temporarily fix pysam on 0.7.8 (0.8.0 fails on Python 3)

Before we figure out what causes this, let's have a working test suite by
fixing pysam on the latest working release.

Traceback:

    Traceback (most recent call last):
      File "/home/travis/build/jamescasbon/PyVCF/build/lib.linux-x86_64-3.3/vcf/test/test_vcf.py", line 1109, in testNoVariantsInRange
        fetched_variants = self.reader.fetch('20', 14370, 17329)
      File "/home/travis/build/jamescasbon/PyVCF/build/lib.linux-x86_64-3.3/vcf/parser.py", line 623, in fetch
        self.reader = self._tabix.fetch(chrom, start, end)
      File "ctabix.pyx", line 345, in pysam.ctabix.Tabixfile.fetch (pysam/ctabix.c:4241)
    TypeError: expected bytes, str found

See #175
Partial support for VCFv4.2

- Add R as an INFO field count (number of alleles including reference).
- Support the optional Source and Version keys on INFO metainformation.

Thanks alot @travc for contributing these fixes!

See #172
Merge pull request #174 from jamescasbon/vcf-4.2

Partial support for VCFv4.2
Bugfix: SNP records with N as ALT now noted as SNPs.

The VCF 4.0 and newer specifications say the ALT field is a comma
separated list that includes "base Strings made up of the bases
A,C,G,T,N". Notably, the last case was not handled by `Record.is_snp`,
causing it to erroneously report `False` for records with "N" as the ALT.
Run tests for Python 3.4.
Merge pull request #177 from gotgenes/bugfix-snps_with_n

Bugfix: SNP records with N as ALT now noted as SNPs.