From e2a996c997ee3933246b60dad108f181ee006d6e Mon Sep 17 00:00:00 2001 From: efischer Date: Tue, 22 Feb 2022 22:23:40 -0600 Subject: [PATCH] update readme --- readme.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/readme.md b/readme.md index d4f7299..3a0504f 100644 --- a/readme.md +++ b/readme.md @@ -159,8 +159,10 @@ Structure: 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 (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. -Writing them to a file lets us generate a graph and its metadata once, then use it for multiple different BiGpairSEQ simulations. +Sample Plate file (to construct the associated occupancy graph). + +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: * 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 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. Metadata about the matching simulation is included as comments. Comments are preceded by `#`.