Our implementation currently uses its own input and output formats.
The parameters:
- -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
- -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