Filtering: vcf_filter.py: added possibility to include a path to custom filters python file, not only a local script file #7
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Don't choke on missing GT
Make metadata RE reluctant (stop on first = not last)
Use requirements files to consolidate dependencies.
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.
Adds _Record.affected_start and .affected_end.
making alternate allele frequency work in the case of non-diploid genotypes
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.
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.
Allow flag INFO field to be declared as string
Don't crash when FORMAT is set to the missing value (.)
The spec actually does not allow for metadata lines without value, but we shouldn't crash on them. Fixes #168
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
- 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
Partial support for VCFv4.2
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.
Bugfix: SNP records with N as ALT now noted as SNPs.
Run tests for Python 3.4.
* Remember the ploidity of uncalled genotypes such that the sample genotypes written by PyVCF.Writer match the sample genotypes read by PyVCF.Reader. * For uncalled _Calls, gt_nums and gt_bases are None; gt_alleles is a list of "None" with a length of _Call.ploidity.
Warning about open file handles muddle the output of unit tests and are a potentially confusing factor to those interpreting the tests.
The sample.data.GT attribute is no longer set to None for uncalled calls, which means that _format_sample can now rely on obtaining the original sample genotype.
Uncalled genotypes support
Fixes #181
Fix double quoting issue when writing VCFs
The issue in 0.8.0 seems to be fixed in 0.8.1, so it's now safe to just blacklist 0.8.0 specifically. See #175
… now it is possible to include a path to custom filters python file
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Sorry, I was trying to include this PR in jamescasbon PyVCF... Better there or better here? :S |
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Better there, I've not looked at this repo in ages. |
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vcf_filter.py: local-script argument changed to custom-filters, since now it is possible to include a path to custom filters python file