| /* The MIT License | |
| Copyright (c) 2014-2016 Genome Research Ltd. | |
| Author: Petr Danecek <[email protected]> | |
| Permission is hereby granted, free of charge, to any person obtaining a copy | |
| of this software and associated documentation files (the "Software"), to deal | |
| in the Software without restriction, including without limitation the rights | |
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| copies of the Software, and to permit persons to whom the Software is | |
| furnished to do so, subject to the following conditions: | |
| The above copyright notice and this permission notice shall be included in | |
| all copies or substantial portions of the Software. | |
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| THE SOFTWARE. | |
| */ | |
| typedef struct _hmm_t hmm_t; | |
| typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob); | |
| /** | |
| * hmm_init() - initialize HMM | |
| * @nstates: number of states | |
| * @tprob: transition probabilities matrix (nstates x nstates), for elements ordering | |
| * see the MAT macro above. | |
| * @ntprob: number of precalculated tprob matrices or 0 for constant probs, independent | |
| * of distance | |
| */ | |
| hmm_t *hmm_init(int nstates, double *tprob, int ntprob); | |
| void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob); | |
| /** | |
| * hmm_init_states() - initial state probabilities | |
| * @probs: initial state probabilities or NULL to reset to default | |
| * | |
| * If uncalled, all states are initialized with the same likelihood | |
| */ | |
| void hmm_init_states(hmm_t *hmm, double *probs); | |
| /** | |
| * hmm_snapshot() - take the model's snapshot, intended for sliding HMM | |
| * @snapshot: NULL or snapshot returned by previous hmm_snapshot() call, must be free()-ed by the caller | |
| * @pos: take the snapshot at this position | |
| * | |
| * If both restore() and snapshot() are needed, restore() must be called first. | |
| */ | |
| void *hmm_snapshot(hmm_t *hmm, void *snapshot, uint32_t pos); | |
| /** | |
| * hmm_restore() - restore model's snapshot, intended for sliding HMM | |
| * @snapshot: snapshot returned by hmm_snapshot() call or NULL to reset | |
| * @isite: take the snapshot at i-th step | |
| * | |
| * If both restore() and snapshot() are needed, restore() must be called first. | |
| */ | |
| void hmm_restore(hmm_t *hmm, void *snapshot); | |
| void hmm_reset(hmm_t *hmm, void *snapshot); | |
| /** | |
| * hmm_get_tprob() - return the array of transition matrices, precalculated | |
| * to ntprob positions. The first matrix is the initial tprob matrix | |
| * set by hmm_init() or hmm_set_tprob() | |
| */ | |
| double *hmm_get_tprob(hmm_t *hmm); | |
| int hmm_get_nstates(hmm_t *hmm); | |
| /** | |
| * hmm_set_tprob_func() - custom setter of transition probabilities | |
| */ | |
| void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data); | |
| /** | |
| * hmm_run_viterbi() - run Viterbi algorithm | |
| * @nsites: number of sites | |
| * @eprob: emission probabilities for each site and state (nsites x nstates) | |
| * @sites: list of positions | |
| * | |
| * When done, hmm->vpath[] contains the calculated Viterbi path. The states | |
| * are indexed starting from 0, a state at i-th site can be accessed as | |
| * vpath[nstates*i]. | |
| */ | |
| void hmm_run_viterbi(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); | |
| /** | |
| * hmm_get_viterbi_path() - the viterbi path: state at ith site is the | |
| * (nstates*isite)-th element | |
| */ | |
| uint8_t *hmm_get_viterbi_path(hmm_t *hmm); | |
| /** | |
| * hmm_run_fwd_bwd() - run the forward-backward algorithm | |
| * @nsites: number of sites | |
| * @eprob: emission probabilities for each site and state (nsites x nstates) | |
| * @sites: list of positions | |
| */ | |
| void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); | |
| /** | |
| * hmm_get_fwd_bwd_prob() - the probability of i-th state at j-th site can | |
| * be accessed as fwd_bwd[j*nstates+i]. | |
| */ | |
| double *hmm_get_fwd_bwd_prob(hmm_t *hmm); | |
| /** | |
| * hmm_run_baum_welch() - run one iteration of Baum-Welch algorithm | |
| * @nsites: number of sites | |
| * @eprob: emission probabilities for each site and state (nsites x nstates) | |
| * @sites: list of positions | |
| * | |
| * Same as hmm_run_fwd_bwd, in addition a pointer to a matrix with the new | |
| * transition probabilities is returned. In this verison, emission | |
| * probabilities are not updated. | |
| */ | |
| double *hmm_run_baum_welch(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites); | |
| void hmm_destroy(hmm_t *hmm); | |