| Age | Commit message (Collapse) | Author |
|---|
|
* gn3/genodb.py (Matrix): Rename to GenotypeMatrix.
(matrix): Update invocation of Matrix.
|
|
* gn3/genodb.py: Document nparray in the module docstring.
(nparray): New function.
|
|
The genotype database now stores the current version of the matrix alone in a
read-optimized form, while storing the older versions of the matrix in a more
compressed form. We are only interested in the current version of the
matrix. So, always use the read optimized storage.
* gn3/genodb.py (Matrix)[row_pointers, column_pointers]: Delete fields.
[array, transpose]: New fields.
* gn3/genodb.py (matrix, row, column): Read from read-optimized storage.
(vector_ref): Delete function.
|
|
* gn3/genodb.py: Remove blank line in module docstring.
|
|
We rewrite genodb using only functions. This makes for much more readable
code.
* gn3/genodb.py: Rewrite without classes.
|
|
* gn3/genodb.py (Matrix.__init__): Retrieve column pointers from database.
(row): Abstract out vector access code to ...
(Matrix.__vector): ... here.
(Matrix.column): New method.
|
|
The genotype database format now supports versioning of matrices. So, we
update genodb.py to return only the most recent genotype matrix.
* gn3/genodb.py (GenotypeDatabase.matrix): Return only the most recent
genotype matrix.
|
|
* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in
read-only mode.
|
|
* gn3/genodb.py (GenotypeDatabase.__init__): Do not create genotype database
if it does not exist.
|
|
It has been decided that the genotype database will use little endianness
wherever applicable.
* gn3/genodb.py (Matrix.__init__): Remove TODO note to decide on endianness.
|
|
* gn3/genodb.py (GenotypeDatabase.get_metadata, GenotypeDatabase.matrix): Do
not terminate database strings with the null character.
|
|
genodb is a tiny library to read our new genotype database file format.
* gn3/genodb.py: New file.
|
