MultipleVariantReader and MultipleVariantIterator

[jmthibault79]

Enables iteration over multiple input files, returning a vector of Variant objects per genomic location.

The vector is reused per location, so the caller must complete processing before continuing iteration, or make a copy.

Strongly inspired by the example of VariantReader/VariantIterator. Merging these Readers or Iterators may be appropriate.

This is an alternative solution to Issue #76

[MauricioCarneiro]

probably better here, but we should have a flag that bypasses this validation (most of the time we will be merging files that were generated by the same tool, thus not needing the time consuming validation).

[MauricioCarneiro]

done reviewing! Great job @jmthibault79 this looks really good. I want @droazen to also take a look. With these important parts of the engine we should be very minutious with the review.

[jmthibault79]

Thanks.

These small commits address your comments except:

• header merging, validation, and bypass flag
• hacky MultipleVariantIterator::operator!=

Travis is still failing, and I'm having trouble parsing the error messages. It would help if we had access to an environment similar to Travis'.

[MauricioCarneiro]

I think your problem is in this line:

std::vector<const std::shared_ptr<bcf_hdr_t>> m_variant_headers; ///< vector of the internal header structures of the variant files

you can't make the std::shared_ptr const because you wouldn't be able to change the reference counting and other things. This is throwing the entire STD library off. See from this error message in Travis:

gamgee/multiple_variant_reader.h:106:49: note: in instantiation of template class 'std::vector<const std::shared_ptr<bcf_hdr_t>, std::allocator<const std::shared_ptr<bcf_hdr_t> > >' requested here
  std::vector<const std::shared_ptr<bcf_hdr_t>> m_variant_headers;  ///< vector of the internal header structures of the variant files

also note from this error line how the typecasting from const shared_ptr to void * is impossible because you would lose constness:

/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../include/c++/4.8/bits/stl_construct.h:75:13: error: static_cast from 'const std::shared_ptr<bcf_hdr_t> *' to 'void *' is not allowed

[jmthibault79]

Thanks for the Travis help. That makes sense. When I change that structure to hold only one header, I'll make sure that it's not const.

[coveralls]

Coverage increased (+1.8%) when pulling 9d1a79b on jt_pqueue into cdafada on master.

[MauricioCarneiro]

woot woot ! we broke the 70% barrier! 👍

[coveralls]

Coverage increased (+1.68%) when pulling 22fa144 on jt_pqueue into fe67107 on master.

[MauricioCarneiro]

has my blessing, next step benchmark it against bcftools!