Support VCF (Variant Call Format)

[Peter]

I have a class that holds a VCF entry (just needs a few tweaks to fit in yat) and a class to parse and modify the header. It probably make sense to create a class for the file itself as well as iterator to allow interaction with STL in std.

[Peter]

(In [3747]) new class for an VCF entry; behaviour of default construction still fluid; refs #905

[Peter]

(In [3750]) refs #905. Adding class VcfHeader? handling the header section in a VCF file.

[Peter]

(In [3759]) refs #905. New class, VcfCompare?, to compare to VCF objects used e.g. in sorting.

[Peter]

(In [3760]) Fix compiler problems with c++98 compiler. Declare functor privately rather than locally. refs #905.

[Peter]

(In [3761]) refs #905. add configure check for boost library iostream

[Peter]

(In [3762]) a first version of new class VcfFile?; refs #905

[Peter]

(In [3763]) refs #905

Some naive tests for class VcfFile?. Also add a test VCF file. If bcftools is available a compressed vcf is generated.

Update README with pointer to set BCFTOOLS via commandline and also mention boost::iostream.

[Peter]

(In [3764]) fix compilation in c++98; use boost::scoped_ptr instead of shared_ptr, which means class in no longer copyable; clarify the compilation error by using boost::noncopyable; refs #905

[Peter]

(In [3765]) add missing include; refs #905

[Peter]

(In [3771]) refs #905; improve docs of VcfFile?; fix so object can be re-opened; add test for that case.

[Peter]

(In [3772]) improve docsin VCF; refs #905

[Peter]

(In [3773]) add function in VcfFile? to read next VCF; refs #905

[Peter]

(In [3774]) implement VcfIterator?. refs #905

[Peter]

In 3789:

refs #905. Avoid #include; prefer forward declaration.

[Peter]

In 3790:

refs #905. Add functionality to access Info.