| Age | Commit message (Expand) | Author |
|---|
| 2022-06-20 | gn3: genodb: Retire get function....* gn3/genodb.py (get): Delete function.
(matrix): Use db.txn.get instead of get.
| Arun Isaac |
| 2022-06-20 | gn3: genodb: Match class and function names of GenotypeMatrix....* gn3/genodb.py (GenotypeMatrix): Match class and function names.
| Arun Isaac |
| 2022-06-20 | gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix....db is unused. nrows and ncols are available in the array and transpose numpy
arrays.
* gn3/genodb.py (GenotypeMatrix)[db, nrows, ncols]: Delete fields.
* gn3/genodb.py (matrix): Do not initialize db, nrows and ncols fields.
| Arun Isaac |
| 2022-06-20 | gn3: genodb: Mention reading entire matrix in module docstring....* gn3/genodb.py: Mention reading entire matrix in module docstring.
| Arun Isaac |
| 2022-06-17 | gn3: genodb: Rename Matrix named tuple to GenotypeMatrix....* gn3/genodb.py (Matrix): Rename to GenotypeMatrix.
(matrix): Update invocation of Matrix.
| Arun Isaac |
| 2022-06-17 | gn3: genodb: Allow retrieval of the entire genotype matrix....* gn3/genodb.py: Document nparray in the module docstring.
(nparray): New function.
| Arun Isaac |
| 2022-06-17 | gn3: genodb: Read optimized storage for the current matrix....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.
| Arun Isaac |
| 2022-06-09 | gn3: genodb: Remove blank line in module docstring....* gn3/genodb.py: Remove blank line in module docstring.
| Arun Isaac |
| 2022-06-09 | gn3: genodb: Rewrite without classes....We rewrite genodb using only functions. This makes for much more readable
code.
* gn3/genodb.py: Rewrite without classes.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Support reading columns....* gn3/genodb.py (Matrix.__init__): Retrieve column pointers from database.
(row): Abstract out vector access code to ...
(Matrix.__vector): ... here.
(Matrix.column): New method.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Read only the most recent genotype matrix....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.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Open genotype database in read-only mode....* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in
read-only mode.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Do not create genotype database if it does not exist....* gn3/genodb.py (GenotypeDatabase.__init__): Do not create genotype database
if it does not exist.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Decide on little endianness....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.
| Arun Isaac |
| 2022-06-08 | gn3: genodb: Do not terminate database strings with null....* gn3/genodb.py (GenotypeDatabase.get_metadata, GenotypeDatabase.matrix): Do
not terminate database strings with the null character.
| Arun Isaac |
| 2022-06-03 | gn3: Add genodb....genodb is a tiny library to read our new genotype database file format.
* gn3/genodb.py: New file.
| Arun Isaac |
