broadinstitute/gamgee — pull request #62 by MauricioCarneiro (2014-06-03 22:02:01+00:00)
Title: Variant: Generic support for fields

Implementation of generic format fields to convert internal binary
format to requested field format. This generic implementation will serve
the needs of both info and format fields, although right now only format
fields are implemented using it (genotype_quals and phred_likelihoods)
as representative of the N=1 and N=many field types.

Summary
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* add VariantField and VariantFieldValue classes to implement the sample level access to the values (former) and the individual value for each sample (latter)
* add random access iterators to VariantField and VariantFieldValue to enable for-each itereation and use of the standard library algorithms as if these were vectors
* add genotype_quals and phred_likelihoods member functions to Variant
* add simple tests to variant_reader (until we have a VariantBuilder to test these independently)

Other minor changes to the framework
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* quiet output for HTSLIB build to remove annoying warnings
* add GQ and PL to test_variants.vcf
* add BCF version of test_variants.vcf (converted with bcftools)
* remove move constructor from stringstream because gcc-4.8 doesn't support it. Added todo to change it back when we are able to update travis to 4.9