broadinstitute/oncotator — pull request #261 by lbergelson (2014-12-09 21:18:03+00:00)
Title: Adding an optional Onp combination stage to oncotator.

this uses OnpCombiner, an InputMutationCreator which wraps any other InputMutationCreator
adjacent SNPs, DNPs, TNPs, etc, will be merged into longer XNPs if they are in the same sample
indels will be unaffected
adding --infer-onps option to Oncotator CLI
closes #13

Adding DNP tests to VariantClassifier Test
There is an issue with splice site straddling dnps, see issue #174

Created SampleNameSelector to choose sample names.
refactored OutputDataManager to use new SampleSelector.

Altered vcf output rendering slightly so that genotype fields are always output if infer-genotypes is specified
fixes issue #247
adding test case for issue #247

Adding __eq__ and __ne__ methods to Annotation and MutationData

Removing redundant methods in MutUtils
replaced isSNP, isInsertion, etc with call to TranscriptProviderUtils.infer_variant_type

Dependencies:
Added 2 pure python dependencies
Adding more-itertools as a dependency
this is a convenient library with useful iterator options like peekable iterators
Adding enum34 as a dependency
this is a backport of enumerations from python 3.4
we should replace strings and string constants with enums

misc:
update to git ignore
adding warning if running maf->vcf without infer genotypes
moved class variables in ConfigTable classes to be member variables instead.
had to revert a small prior change to vcf.out.config, it wasn't doing what it was intended to do
adding a more informative log message about temporary files in OutputDataManager.
removing empty file AliasManager