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Update readme with CLI arguments

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efischer
2022-02-27 16:56:58 -06:00
parent b1155f8100
commit e10350c214
1 changed files with 9 additions and 3 deletions
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@@ -48,8 +48,13 @@ For example, to run the program with 32 gigabytes of memory, use the command:
`java -Xmx32G -jar BiGpairSEQ_Sim.jar` `java -Xmx32G -jar BiGpairSEQ_Sim.jar`
Once running, BiGpairSEQ_Sim has an interactive, menu-driven CLI for generating files and simulating TCR pairing. The There are a number of command line options, to allow the program to be used in shell scripts. For a full list,
main menu looks like this: use the -help flag:
`java -jar BiGpairSEQ_SIM -help`
If no command line arguments are given, BiGpairSEQ_Sim will launch with an interactive, menu-driven CLI for
generating files and simulating TCR pairing. The main menu looks like this:
``` ```
--------BiGPairSEQ SIMULATOR-------- --------BiGPairSEQ SIMULATOR--------
@@ -78,6 +83,7 @@ By default, the Options menu looks like this:
0) Return to main menu 0) Return to main menu
``` ```
### INPUT/OUTPUT ### INPUT/OUTPUT
To run the simulation, the program reads and writes 4 kinds of files: To run the simulation, the program reads and writes 4 kinds of files:
@@ -290,7 +296,7 @@ slightly less time than the simulation itself. Real elapsed time from start to f
* ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE * ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
* ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED * ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED
* Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix. * Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.
* Re-implement command line arguments, to enable scripting and statistical simulation studies * ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE
* Re-implement CDR1 matching method * Re-implement CDR1 matching method
* Implement Duan and Su's maximum weight matching algorithm * Implement Duan and Su's maximum weight matching algorithm
* Add controllable algorithm-type parameter? * Add controllable algorithm-type parameter?