1 files changed, 0 insertions, 107 deletions
diff --git a/debian/vendor-h2o/deps/klib/khmm.h b/debian/vendor-h2o/deps/klib/khmm.h
deleted file mode 100644
index d87673b..0000000
--- a/debian/vendor-h2o/deps/klib/khmm.h
+++ /dev/null
@@ -1,107 +0,0 @@
-#ifndef AC_SCHMM_H_
-#define AC_SCHMM_H_
-
-/*
- * Last Modified: 2008-03-10
- * Version: 0.1.0-8
- *
- * 2008-03-10, 0.1.0-8: make icc report two more "VECTORIZED"
- * 2008-03-10, 0.1.0-7: accelerate for some CPU
- * 2008-02-07, 0.1.0-6: simulate sequences
- * 2008-01-15, 0.1.0-5: goodness of fit
- * 2007-11-20, 0.1.0-4: add function declaration of hmm_post_decode()
- * 2007-11-09: fix a memory leak
- */
-
-#include <stdlib.h>
-
-#define HMM_VERSION "0.1.0-7"
-
-#define HMM_FORWARD  0x02
-#define HMM_BACKWARD 0x04
-#define HMM_VITERBI  0x40
-#define HMM_POSTDEC  0x80
-
-#ifndef FLOAT
-#define FLOAT double
-#endif
-#define HMM_TINY     1e-25
-#define HMM_INF      1e300
-
-typedef struct
-{
-	int m, n; // number of symbols, number of states
-	FLOAT **a, **e; // transition matrix and emitting probilities
-	FLOAT **ae; // auxiliary array for acceleration, should be calculated by hmm_pre_backward()
-	FLOAT *a0; // trasition matrix from the start state
-} hmm_par_t;
-
-typedef struct
-{
-	int L;
-	unsigned status;
-	char *seq;
-	FLOAT **f, **b, *s;
-	int *v; // Viterbi path
-	int *p; // posterior decoding
-} hmm_data_t;
-
-typedef struct
-{
-	int m, n;
-	FLOAT Q0, **A, **E, *A0;
-} hmm_exp_t;
-
-typedef struct
-{
-	int l, *obs;
-	FLOAT *thr;
-} hmm_gof_t;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-	/* initialize and destroy hmm_par_t */
-	hmm_par_t *hmm_new_par(int m, int n);
-	void hmm_delete_par(hmm_par_t *hp);
-	/* initialize and destroy hmm_data_t */
-	hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp);
-	void hmm_delete_data(hmm_data_t *hd);
-	/* initialize and destroy hmm_exp_t */
-	hmm_exp_t *hmm_new_exp(const hmm_par_t *hp);
-	void hmm_delete_exp(hmm_exp_t *he);
-	/* Viterbi, forward and backward algorithms */
-	FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd);
-	void hmm_pre_backward(hmm_par_t *hp);
-	void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd);
-	void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd);
-	/* log-likelihood of the observations (natural based) */
-	FLOAT hmm_lk(const hmm_data_t *hd);
-	/* posterior probability at the position on the sequence */
-	FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob);
-	/* posterior decoding */
-	void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd);
-	/* expected counts of transitions and emissions */
-	hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd);
-	/* add he0 counts to he1 counts*/
-	void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1);
-	/* the Q function that should be maximized in EM */
-	FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he);
-	FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he);
-	/* simulate sequences */
-	char *hmm_simulate(const hmm_par_t *hp, int L);
-#ifdef __cplusplus
-}
-#endif
-
-static inline void **calloc2(int n_row, int n_col, int size)
-{
-	char **p;
-	int k;
-	p = (char**)malloc(sizeof(char*) * n_row);
-	for (k = 0; k != n_row; ++k)
-		p[k] = (char*)calloc(n_col, size);
-	return (void**)p;
-}
-
-#endif