Usage (command-line)

For the CLI app v0.1.4, usage is pretty simple being one of:

java -jar ../../jarfiles/CLI-app-v0.1.4.jar <mask> <ancestral> <output> <mainfiles>
java -jar ../../jarfiles/CLI-app-v0.1.4.jar <mask> <ancestral> <output> <mainfiles> <ratio>
java -jar ../../jarfiles/CLI-app-v0.1.4.jar <mask> <ancestral> <output> <mainfiles> <bootstraps>
java -jar ../../jarfiles/CLI-app-v0.1.4.jar <mask> <ancestral> <output> <mainfiles> <bootstraps> <ratio>

Where: - Mask is a file containing one or more masklines. These are usually generated by the maskGenerator (hardcoded for now; runnable entrypoint TODO #18, but see the maskfiles in the examples folder) - Ancestral file is a .fasta containing the outgroup - Output is where main output will go (must be writable) - Fileslist is a comma-separated list of one or more main (focal) alignments - The next argument can (in the 5-arg version) be either an integer (interpreted as number of boostraps), or double (neutral ratio). - Alternatively for the 6-arg case, args 5 and 6 are parsed to the bootstrap replicates and ratio, respectively

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Verbose mode debugs are supported by prepending 'true' to the argument list, e.g. java -jar ../../jarfiles/CLI-app-v0.1.4.jar true <mask> <ancestral> <output> <mainfiles> java -jar ../../jarfiles/CLI-app-v0.1.4.jar true <mask> <ancestral> <output> <mainfiles> <ratio> java -jar ../../jarfiles/CLI-app-v0.1.4.jar true <mask> <ancestral> <output> <mainfiles> <bootstraps> java -jar ../../jarfiles/CLI-app-v0.1.4.jar true <mask> <ancestral> <output> <mainfiles> <bootstraps> <ratio>