alimanfoo
Wish: support for writing in vcflib's binding
The reason for this request is to enable possibly filtering and manipulation like you can do with PyVCF, but with a much faster (numpy + C++ backend) interface.
I wrote "in vcflib's binding" rather to vcfnp itself because I think that pushing data from numpy to VCF wouldn't be exactly trivial, also considering that vcfnp parses the various bits of a VCF file independently.
Inspecting vcflib's source code shows that there are no methods to explicitly write a file, since the results of manipulations are outputted as streams.
Yes, as far as I can make out there is no explicit support in the vcflib C++ API for writing a VCF. If ekg adds this upstream I'd be happy to wrap it in the vcflib cython extension.
In data giovedì 23 maggio 2013 05:46:29, Alistair Miles ha scritto:
Yes, as far as I can make out there is no explicit support in the vcflib C++ API for writing a VCF. If ekg adds this upstream I'd be happy to wrap it in
By looking at the code of some of the utilties in vcflib, I see that simply put the header is written to stdout first, then vectors representing records are simply sent to stdout.
I wonder how hard would it be to add a fstream operator to vcflib in addition to ostream that's arelady implemented.
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