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update readme

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efischer
2022-02-22 22:23:40 -06:00
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@@ -159,8 +159,10 @@ Structure:
Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file
(to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a (to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a
Sample Plate file (to construct the associated occupancy graph). These files can be several gigabytes in size. Sample Plate file (to construct the associated occupancy graph).
Writing them to a file lets us generate a graph and its metadata once, then use it for multiple different BiGpairSEQ simulations.
These files can be several gigabytes in size. Writing them to a file lets us generate a graph and its metadata once,
then use it for multiple different BiGpairSEQ simulations.
Options for creating a Graph and Data file: Options for creating a Graph and Data file:
* The Cell Sample file to use * The Cell Sample file to use
@@ -172,7 +174,11 @@ portable data format may be implemented in the future. The tricky part is encodi
--- ---
#### Matching Results Files #### Matching Results Files
Matching results files consist of the results of a BiGpairSEQ matching simulation. Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a Graph and
Data file. To save file I/O time, the data from the most recent Graph and Data file read or generated is cached
by the simulator. Subsequent BiGpairSEQ simulations run with the same input filename will use the cached version
rather than reading in again from disk.
Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details. Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
Metadata about the matching simulation is included as comments. Comments are preceded by `#`. Metadata about the matching simulation is included as comments. Comments are preceded by `#`.