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Ran 01 Aug 2014 02:40AM UTC

Files 60

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Committed 01 Aug 2014 02:32AM UTC coverage: 73.675% (-0.02%) from 73.693%

Job # 584.1

Build Type

push

travis-ci

Committed by

MauricioCarneiro

Commit Message

Variant: read api for format field strings

There was a bug with the implementation that wasn't concordant with how
htslib parses the strings in the bcf1_t structure. It now works by
checking for bcf_string_vector_end values to separate the strings, and
skips blocks to find the values for every sample using the fixed length
blocks as defined by bcf_fmt_t->n.

Support for vector of strings per sample is not yet agreed upon in the
VCF/BCF spec, so comma separated strings will be treated as a single
string by htslib and thus by Gamgee.

* string type number of bytes per value is reported by fmt->n (weirdly)
* make format utility functions not inline (too big to inline)
* add tests for variable length strings across samples
* add functional tests for iterators of VariantField<VariantFieldValue<string>>
* add tests for all type conversions in the format field api

fixes #78

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