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Adding the second VcfParser class: NucleusParser  (#346)

* Add NucleusParser class

as the second class that implements the VcfParser interface.

Currently we are trying to solve a few issues related to the nucleus Wheel file.

* Adding the second VcfParser class: NucleusParser

After defining the VCFParser interface and PyVcfParser in the PR we add
NucleusParser. Following points must be considered:
 * This new parser is hidden behind a flag (use_nucleus=False).
 * Since we are not still able to create a Wheel file that have the
 from_string() method, we use a hack to make Nucleus work: write the whole
 file to a local temp file and send it as input to parser.
 * Currently we don't have any unit tests or integration test. We
 manually cheked the sanity of Nucleus output by comparing its output
 table with PyVcf output. This must be done in the next step.

* Avoid failing builds due to missing nucleus module

as proposed by Asha.

* First round of comments

* Adding from_string() to NucleusParser

After we managed to build a Wheel file based on the latest code base.
We also make a few minor changes to make NucleusParser work with Dataflow.

* Second round of comments

* Add unit tests for NucleusParser

and also move unit tests of Variant and VariantCall classes to vcf_parser_test.py

* A temporary solution to make the Travis build pass

In order to use NucleusParser with a DataflowRuner the following flag is
still needed:
--extra_package /dirctory/containing/Nucleus-0.1.0-py2-none-any.whl

* Next round of comments

5887 of 6682 relevant lines covered (88.1%)

0.88 hits per line

Jobs
ID Job ID Ran Files Coverage
1 1265.1 0
88.1
 Travis Job 1265.1
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