Rename positions to sequence_positions in SNPDatabase

VCF locations are relative to the start of the sequence for each entry.
Rename positions to sequence_positions to make this less ambiguous.

Change-Id: Iaff9eb454ced2231764b45af6c12ed545a4bdf2c

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18481646]
Add missing include file to primitives_inl.h

Change-Id: Iad4cb411f2dcc8317c486ac4e3801afa8b3e6344
nvbio::max requires nvbio/basic/numbers.h to be included first

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18481647]
added recent news

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18481853]
make sure all code compiles on compute capability < 3.5, even if unsupported

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18481906]
added paired-end cmdline

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18481946]
added implicit conversion operators to the plain-view type

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18483651]
specified the type for size()

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18483660]
new sequence data module, to replace the old io/reads:

 - cleaned up interfaces
 - added handling of multiple alphabets
 - added reuse of SequenceData containers during input

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484040]
changed the SequenceDataStream interface to just receive an encoder

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484114]
fixed member name

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484118]
added constants

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484124]
fixed template parameter

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484128]
removed spurious semicolon

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484150]
fixed type name

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484154]
fixed method signature

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484157]
fixed base class

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484189]
added a begin_batch() method to clear the encoders

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484205]
added missing virtual method qualifier

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484219]
fixed type names

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484220]
added copy constructor and copy operators that are not implicitly found in the base class

[git-p4: depot-paths = "//sw/gpgpu/nvbio/main/": change = 18484252]