[FORMATS-142] Replace NucleotideContigFragment with Sequence and Slice

[heuermh]

Fixes #142

Mapped NucleotideContigFragment fields:

contigName --> name
contigLength --> totalLength
description --> description
sequence --> sequence
index --> index
start --> start
end --> end
length --> length
fragments --> slices

Unmapped NucleotideContigFragment fields:

None

Unmapped Slice fields:

alphabet
strand
attributes

This will allow refactoring the org.bdgenomics.adam.rdd.contig package in ADAM to org.bdgenomics.adam.rdd.sequence with not much more than class and field renames.

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Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/171/ Test PASSed.

[AmplabJenkins]

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/183/ Test PASSed.

[AmplabJenkins]

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/186/ Test PASSed.