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Diffstat (limited to 'topics/genotype-database.gmi')
| -rw-r--r-- | topics/genotype-database.gmi | 22 |
1 files changed, 16 insertions, 6 deletions
diff --git a/topics/genotype-database.gmi b/topics/genotype-database.gmi index 9dee8a7..1ca4bb0 100644 --- a/topics/genotype-database.gmi +++ b/topics/genotype-database.gmi @@ -45,8 +45,11 @@ LMDB maps octet vector keys to octet vector values. Any data we put into a LMDB The basic unit of storage in the database is a blob. A BLOB is an octet vector PAYLOAD with associated METADATA. To store a blob in the database, we first compute its HASH, and then put PAYLOAD into the database as a <HASH, PAYLOAD> key-value pair. HASH is the SHA256 hash of BLOB (both the octet vector payload and its associated metadata). To compute HASH, we first serialize BLOB into a series of octets, and then hash the resulting octet vector. Precisely, if BLOB contains PAYLOAD and is associated with (KEY, VALUE),... pairs of metadata, then hash(BLOB) is given by ``` -BLOB = blob(payload=PAYLOAD, metadata=[(KEY, VALUE),...]) -hash(BLOB) = SHA256(concatenate(length(BLOB.payload), BLOB.payload, [length(BLOB.metadata.KEY), BLOB.metadata.KEY, length(BLOB.metadata.VALUE), BLOB.metadata.VALUE],...)) +BLOB = blob(payload=PAYLOAD, + metadata=[(KEY, VALUE),...]) +hash(BLOB) = SHA256(concatenate(length(BLOB.payload), BLOB.payload, + [length(BLOB.metadata.KEY), BLOB.metadata.KEY, + length(BLOB.metadata.VALUE), BLOB.metadata.VALUE],...)) ``` This encoding of BLOB into octets is one-to-one. So, assuming there are no hash collisions, every BLOB is uniquely mapped to a HASH. @@ -58,22 +61,29 @@ We store every version of the genotype matrix in the database, each version as a ``` ROW = blob(payload=ROW-VECTOR, metadata=[]) COLUMN = blob(payload=COLUMN-VECTOR, metadata=[]) -MATRIX = blob(payload=concatenate(concatenate(hash(ROW1), hash(ROW2),...), concatenate(hash(COLUMN1), hash(COLUMN2),...)), metadata=[("nrows", NUMBER-OF-ROWS), ("ncols", NUMBER-OF-COLUMNS)]) +MATRIX = blob(payload=concatenate(concatenate(hash(ROW1), hash(ROW2),...), + concatenate(hash(COLUMN1), hash(COLUMN2),...)), + metadata=[("nrows", NUMBER-OF-ROWS), + ("ncols", NUMBER-OF-COLUMNS)]) ``` We repeat this for every version of the genotype matrix, and associate the concatenated hashes of all the matrix blobs with the "all-versions" key by mutation. ``` -put(key="all-versions", value=concatenate(hash(MATRIX1), hash(MATRIX2),...)) +put(key="all-versions", + value=concatenate(hash(MATRIX1), hash(MATRIX2),...)) ``` ### Fast storage for the current matrix We store two additional copies of the current matrix for fast retrieval. This read-optimized version of the matrix is, essentialy, the matrix in its row-major and column-major forms. The row-major form facilitates fast row reads, and the column-major form facilitates fast column reads. If MATRIX0 is the most recent matrix, then the blob CURRENT_MATRIX stored in the database is given by the following. ``` -CURRENT_MATRIX = blob(concatenate(row-major-encoding(MATRIX0), row-major-encoding(transpose(MATRIX0))), metadata=[("matrix", hash(MATRIX0))]) +CURRENT_MATRIX = blob(payload=concatenate(row-major-encoding(MATRIX0), + row-major-encoding(transpose(MATRIX0))), + metadata=[("matrix", hash(MATRIX0))]) ``` The hash of CURRENT_MATRIX is associated with the "current" key by mutation. ``` -put(key="current", value=hash(CURRENT_MATRIX)) +put(key="current", + value=hash(CURRENT_MATRIX)) ``` ### Design notes |