* -E,--weight
* -W,--window-size
* -H,--hmm
* -S,--sequence
* -h,--help
* -m,--low-memory
* -M,--high-memory
* -TO,--table-file-output
* -TI,--table-file-input
* -F,--fancy-output
* -NF,--no-fancy-output
* -V,--viterbi
* -B,--beam-width
* -P,--parameters-file
* -I,--hints-file
* -F,--hints-fuzz
* -A,--sample
* -R,--precision
* -O,--posterior
* -R,--posterior-file
* -I,--incorrect-model
* -E,--weight <float> - take one argument, the penalty $\gamma$ for the HERD algorithm.
* -W,--window-size <integer> - size of the window $W$
* -H,--hmm <file> - the file in which is HMM
* -S,--sequence <file> - file containing input sequences, one sequence per line
* -m,--low-memory - if set, herd will use checkpointig technique to reduce memory requirements.
* -M,--high-memory - omit checkpointing technique
* -TO,--table-file-output <file> - store the precomputed posterior values to the file
* -TI,--table-file-input <file> - instead of computing the posterior values load them from file
* -F,--fancy-output - nice output
* -NF,--no-fancy-output - output as a sequence of labels
* -V,--viterbi - use viterbi algorithm insted of herd
* -B,--beam-width - Beam width for Viterbi algorithm (currently not implemented)
* -P,--parameters-file <file> - file containing the list of parameters
* -I,--hints-file <file> - file containing hints for the HERD algorithm to reduce running time
* -F,--hints-fuzz <integer> - the parameters for fuzzier hints.
* -A,--sample <file-prefix> <from> <to> - generate sequences and annotation from the model, save them
* -R,--precision <logoudble/logfloat/double/float> - which precision to use
* -O,--posterior - the posterior reward for the gain function
* -I,--incorrect-model - do not simplify the jpHMM
This page was created by Michal Nánási
