1 files changed, 0 insertions, 423 deletions

diff --git a/debian/vendor-h2o/deps/klib/khmm.c b/debian/vendor-h2o/deps/klib/khmm.c
deleted file mode 100644
index 711ade5..0000000
--- a/debian/vendor-h2o/deps/klib/khmm.c
+++ /dev/null
@@ -1,423 +0,0 @@
-#include <math.h>
-#include <stdio.h>
-#include <assert.h>
-#include <string.h>
-#include <stdlib.h>
-#include "khmm.h"
-
-// new/delete hmm_par_t
-
-hmm_par_t *hmm_new_par(int m, int n)
-{
-	hmm_par_t *hp;
-	int i;
-	assert(m > 0 && n > 0);
-	hp = (hmm_par_t*)calloc(1, sizeof(hmm_par_t));
-	hp->m = m; hp->n = n;
-	hp->a0 = (FLOAT*)calloc(n, sizeof(FLOAT));
-	hp->a = (FLOAT**)calloc2(n, n, sizeof(FLOAT));
-	hp->e = (FLOAT**)calloc2(m + 1, n, sizeof(FLOAT));
-	hp->ae = (FLOAT**)calloc2((m + 1) * n, n, sizeof(FLOAT));
-	for (i = 0; i != n; ++i) hp->e[m][i] = 1.0;
-	return hp;
-}
-void hmm_delete_par(hmm_par_t *hp)
-{
-	int i;
-	if (hp == 0) return;
-	for (i = 0; i != hp->n; ++i) free(hp->a[i]);
-	for (i = 0; i <= hp->m; ++i) free(hp->e[i]);
-	for (i = 0; i < (hp->m + 1) * hp->n; ++i) free(hp->ae[i]);
-	free(hp->a); free(hp->e); free(hp->a0); free(hp->ae);
-	free(hp);
-}
-
-// new/delete hmm_data_t
-
-hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp)
-{
-	hmm_data_t *hd;
-	hd = (hmm_data_t*)calloc(1, sizeof(hmm_data_t));
-	hd->L = L;
-	hd->seq = (char*)malloc(L + 1);
-	memcpy(hd->seq + 1, seq, L);
-	return hd;
-}
-void hmm_delete_data(hmm_data_t *hd)
-{
-	int i;
-	if (hd == 0) return;
-	for (i = 0; i <= hd->L; ++i) {
-		if (hd->f) free(hd->f[i]);
-		if (hd->b) free(hd->b[i]);
-	}
-	free(hd->f); free(hd->b); free(hd->s); free(hd->v); free(hd->p); free(hd->seq);
-	free(hd);
-}
-
-// new/delete hmm_exp_t
-
-hmm_exp_t *hmm_new_exp(const hmm_par_t *hp)
-{
-	hmm_exp_t *he;
-	assert(hp);
-	he = (hmm_exp_t*)calloc(1, sizeof(hmm_exp_t));
-	he->m = hp->m; he->n = hp->n;
-	he->A0 = (FLOAT*)calloc(hp->n, sizeof(FLOAT));
-	he->A = (FLOAT**)calloc2(hp->n, hp->n, sizeof(FLOAT));
-	he->E = (FLOAT**)calloc2(hp->m + 1, hp->n, sizeof(FLOAT));
-	return he;
-}
-void hmm_delete_exp(hmm_exp_t *he)
-{
-	int i;
-	if (he == 0) return;
-	for (i = 0; i != he->n; ++i) free(he->A[i]);
-	for (i = 0; i <= he->m; ++i) free(he->E[i]);
-	free(he->A); free(he->E); free(he->A0);
-	free(he);
-}
-
-// Viterbi algorithm
-
-FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd)
-{
-	FLOAT **la, **le, *preV, *curV, max;
-	int **Vmax, max_l; // backtrace matrix
-	int k, l, b, u;
-	
-	if (hd->v) free(hd->v);
-	hd->v = (int*)calloc(hd->L+1, sizeof(int));
-	la = (FLOAT**)calloc2(hp->n, hp->n, sizeof(FLOAT));
-	le = (FLOAT**)calloc2(hp->m + 1, hp->n, sizeof(FLOAT));
-	Vmax = (int**)calloc2(hd->L+1, hp->n, sizeof(int));
-	preV = (FLOAT*)malloc(sizeof(FLOAT) * hp->n);
-	curV = (FLOAT*)malloc(sizeof(FLOAT) * hp->n);
-	for (k = 0; k != hp->n; ++k)
-		for (l = 0; l != hp->n; ++l)
-			la[k][l] = log(hp->a[l][k]); // this is not a bug
-	for (b = 0; b != hp->m; ++b)
-		for (k = 0; k != hp->n; ++k)
-			le[b][k] = log(hp->e[b][k]);
-	for (k = 0; k != hp->n; ++k) le[hp->m][k] = 0.0;
-	// V_k(1)
-	for (k = 0; k != hp->n; ++k) {
-		preV[k] = le[(int)hd->seq[1]][k] + log(hp->a0[k]);
-		Vmax[1][k] = 0;
-	}
-	// all the rest
-	for (u = 2; u <= hd->L; ++u) {
-		FLOAT *tmp, *leu = le[(int)hd->seq[u]];
-		for (k = 0; k != hp->n; ++k) {
-			FLOAT *laa = la[k];
-			for (l = 0, max = -HMM_INF, max_l = -1; l != hp->n; ++l) {
-				if (max < preV[l] + laa[l]) {
-					max = preV[l] + laa[l];
-					max_l = l;
-				}
-			}
-			assert(max_l >= 0); // cannot be zero
-			curV[k] = leu[k] + max;
-			Vmax[u][k] = max_l;
-		}
-		tmp = curV; curV = preV; preV = tmp; // swap
-	}
-	// backtrace
-	for (k = 0, max_l = -1, max = -HMM_INF; k != hp->n; ++k) {
-		if (max < preV[k]) {
-			max = preV[k]; max_l = k;
-		}
-	}
-	assert(max_l >= 0); // cannot be zero
-	hd->v[hd->L] = max_l;
-	for (u = hd->L; u >= 1; --u)
-		hd->v[u-1] = Vmax[u][hd->v[u]];
-	for (k = 0; k != hp->n; ++k) free(la[k]);
-	for (b = 0; b < hp->m; ++b) free(le[b]);
-	for (u = 0; u <= hd->L; ++u) free(Vmax[u]);
-	free(la); free(le); free(Vmax); free(preV); free(curV);
-	hd->status |= HMM_VITERBI;
-	return max;
-}
-
-// forward algorithm
-
-void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd)
-{
-	FLOAT sum, tmp, **at;
-	int u, k, l;
-	int n, m, L;
-	assert(hp && hd);
-	// allocate memory for hd->f and hd->s
-	n = hp->n; m = hp->m; L = hd->L;
-	if (hd->s) free(hd->s);
-	if (hd->f) { 
-		for (k = 0; k <= hd->L; ++k) free(hd->f[k]);
-		free(hd->f);
-	}
-	hd->f = (FLOAT**)calloc2(hd->L+1, hp->n, sizeof(FLOAT));
-	hd->s = (FLOAT*)calloc(hd->L+1, sizeof(FLOAT));
-	hd->status &= ~(unsigned)HMM_FORWARD;
-	// at[][] array helps to improve the cache efficiency
-	at = (FLOAT**)calloc2(n, n, sizeof(FLOAT));
-	// transpose a[][]
-	for (k = 0; k != n; ++k)
-		for (l = 0; l != n; ++l)
-			at[k][l] = hp->a[l][k];
-	// f[0], but it should never be used
-	hd->s[0] = 1.0;
-	for (k = 0; k != n; ++k) hd->f[0][k] = 0.0;
-	// f[1]
-	for (k = 0, sum = 0.0; k != n; ++k)
-		sum += (hd->f[1][k] = hp->a0[k] * hp->e[(int)hd->seq[1]][k]);
-	for (k = 0; k != n; ++k) hd->f[1][k] /= sum;
-	hd->s[1] = sum;
-	// f[2..hmmL], the core loop
-	for (u = 2; u <= L; ++u) {
-		FLOAT *fu = hd->f[u], *fu1 = hd->f[u-1], *eu = hp->e[(int)hd->seq[u]];
-		for (k = 0, sum = 0.0; k != n; ++k) {
-			FLOAT *aa = at[k];
-			for (l = 0, tmp = 0.0; l != n; ++l) tmp += fu1[l] * aa[l];
-			sum += (fu[k] = eu[k] * tmp);
-		}
-		for (k = 0; k != n; ++k) fu[k] /= sum;
-		hd->s[u] = sum;
-	}
-	// free at array
-	for (k = 0; k != hp->n; ++k) free(at[k]);
-	free(at);
-	hd->status |= HMM_FORWARD;
-}
-
-//  precalculate hp->ae
-
-void hmm_pre_backward(hmm_par_t *hp)
-{
-	int m, n, b, k, l;
-	assert(hp);
-	m = hp->m; n = hp->n;
-	for (b = 0; b <= m; ++b) {
-		for (k = 0; k != n; ++k) {
-			FLOAT *p = hp->ae[b * hp->n + k];
-			for (l = 0; l != n; ++l)
-				p[l] = hp->e[b][l] * hp->a[k][l];
-		}
-	}
-}
-
-// backward algorithm
-
-void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd)
-{
-	FLOAT tmp;
-	int k, l, u;
-	int m, n, L;
-	assert(hp && hd);
-	assert(hd->status & HMM_FORWARD);
-	// allocate memory for hd->b
-	m = hp->m; n = hp->n; L = hd->L;
-	if (hd->b) { 
-		for (k = 0; k <= hd->L; ++k) free(hd->b[k]);
-		free(hd->b);
-	}
-	hd->status &= ~(unsigned)HMM_BACKWARD;
-	hd->b = (FLOAT**)calloc2(L+1, hp->n, sizeof(FLOAT));
-	// b[L]
-	for (k = 0; k != hp->n; ++k) hd->b[L][k] = 1.0 / hd->s[L];
-	// b[1..L-1], the core loop
-	for (u = L-1; u >= 1; --u) {
-		FLOAT *bu1 = hd->b[u+1], **p = hp->ae + (int)hd->seq[u+1] * n;
-		for (k = 0; k != n; ++k) {
-			FLOAT *q = p[k];
-			for (l = 0, tmp = 0.0; l != n; ++l) tmp += q[l] * bu1[l];
-			hd->b[u][k] = tmp / hd->s[u];
-		}
-	}
-	hd->status |= HMM_BACKWARD;
-	for (l = 0, tmp = 0.0; l != n; ++l)
-		tmp += hp->a0[l] * hd->b[1][l] * hp->e[(int)hd->seq[1]][l];
-	if (tmp > 1.0 + 1e-6 || tmp < 1.0 - 1e-6) // in theory, tmp should always equal to 1
-		fprintf(stderr, "++ Underflow may have happened (%lg).\n", tmp);
-}
-
-// log-likelihood of the observation
-
-FLOAT hmm_lk(const hmm_data_t *hd)
-{
-    FLOAT sum = 0.0, prod = 1.0;
-	int u, L;
-	L = hd->L;
-	assert(hd->status & HMM_FORWARD);
-	for (u = 1; u <= L; ++u) {
-		prod *= hd->s[u];
-		if (prod < HMM_TINY || prod >= 1.0/HMM_TINY) { // reset
-			sum += log(prod);
-			prod = 1.0;
-		}
-	}
-	sum += log(prod);
-	return sum;
-}
-
-// posterior decoding
-
-void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd)
-{
-	int u, k;
-	assert(hd->status && HMM_BACKWARD);
-	if (hd->p) free(hd->p);
-	hd->p = (int*)calloc(hd->L + 1, sizeof(int));
-	for (u = 1; u <= hd->L; ++u) {
-		FLOAT prob, max, *fu = hd->f[u], *bu = hd->b[u], su = hd->s[u];
-		int max_k;
-		for (k = 0, max = -1.0, max_k = -1; k != hp->n; ++k) {
-			if (max < (prob = fu[k] * bu[k] * su)) {
-				max = prob; max_k = k;
-			}
-		}
-		assert(max_k >= 0);
-		hd->p[u] = max_k;
-	}
-	hd->status |= HMM_POSTDEC;
-}
-
-// posterior probability of states
-
-FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob)
-{
-	FLOAT sum = 0.0, ss = hd->s[u], *fu = hd->f[u], *bu = hd->b[u];
-	int k;
-	for (k = 0; k != hp->n; ++k)
-		sum += (prob[k] = fu[k] * bu[k] * ss);
-	return sum; // in theory, this should always equal to 1.0
-}
-
-// expected counts
-
-hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd)
-{
-	int k, l, u, b, m, n;
-	hmm_exp_t *he;
-	assert(hd->status & HMM_BACKWARD);
-	he = hmm_new_exp(hp);
-	// initialization
-	m = hp->m; n = hp->n;
-	for (k = 0; k != n; ++k)
-		for (l = 0; l != n; ++l) he->A[k][l] = HMM_TINY;
-	for (b = 0; b <= m; ++b)
-		for (l = 0; l != n; ++l) he->E[b][l] = HMM_TINY;
-	// calculate A_{kl} and E_k(b), k,l\in[0,n)
-	for (u = 1; u < hd->L; ++u) {
-		FLOAT *fu = hd->f[u], *bu = hd->b[u], *bu1 = hd->b[u+1], ss = hd->s[u];
-		FLOAT *Ec = he->E[(int)hd->seq[u]], **p = hp->ae + (int)hd->seq[u+1] * n;
-		for (k = 0; k != n; ++k) {
-			FLOAT *q = p[k], *AA = he->A[k], fuk = fu[k];
-			for (l = 0; l != n; ++l) // this is cache-efficient
-				AA[l] += fuk * q[l] * bu1[l];
-			Ec[k] += fuk * bu[k] * ss;
-		}
-	}
-	// calculate A0_l
-	for (l = 0; l != n; ++l)
-		he->A0[l] += hp->a0[l] * hp->e[(int)hd->seq[1]][l] * hd->b[1][l];
-	return he;
-}
-
-FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he)
-{
-	int k, l, b;
-	FLOAT sum = 0.0;
-	for (k = 0; k != hp->n; ++k) {
-		FLOAT tmp;
-		for (b = 0, tmp = 0.0; b != hp->m; ++b) tmp += he->E[b][k];
-		for (b = 0; b != hp->m; ++b)
-			sum += he->E[b][k] * log(he->E[b][k] / tmp);
-	}
-	for (k = 0; k != hp->n; ++k) {
-		FLOAT tmp, *A = he->A[k];
-		for (l = 0, tmp = 0.0; l != hp->n; ++l) tmp += A[l];
-		for (l = 0; l != hp->n; ++l) sum += A[l] * log(A[l] / tmp);
-	}
-	return (he->Q0 = sum);
-}
-
-// add he0 to he1
-
-void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1)
-{
-	int b, k, l;
-	assert(he0->m == he1->m && he0->n == he1->n);
-	for (k = 0; k != he1->n; ++k) {
-		he1->A0[k] += he0->A0[k];
-		for (l = 0; l != he1->n; ++l)
-			he1->A[k][l] += he0->A[k][l];
-	}
-	for (b = 0; b != he1->m; ++b) {
-		for (l = 0; l != he1->n; ++l)
-			he1->E[b][l] += he0->E[b][l];
-	}
-}
-
-// the EM-Q function
-
-FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he)
-{
-	FLOAT sum = 0.0;
-	int bb, k, l;
-	for (bb = 0; bb != he->m; ++bb) {
-		FLOAT *eb = hp->e[bb], *Eb = he->E[bb];
-		for (k = 0; k != hp->n; ++k) {
-			if (eb[k] <= 0.0) return -HMM_INF;
-			sum += Eb[k] * log(eb[k]);
-		}
-	}
-	for (k = 0; k != he->n; ++k) {
-		FLOAT *Ak = he->A[k], *ak = hp->a[k];
-		for (l = 0; l != he->n; ++l) {
-			if (ak[l] <= 0.0) return -HMM_INF;
-			sum += Ak[l] * log(ak[l]);
-		}
-	}
-	return (sum -= he->Q0);
-}
-
-// simulate sequence
-
-char *hmm_simulate(const hmm_par_t *hp, int L)
-{
-	int i, k, l, b;
-	FLOAT x, y, **et;
-	char *seq;
-	seq = (char*)calloc(L+1, 1);
-	// calculate the transpose of hp->e[][]
-	et = (FLOAT**)calloc2(hp->n, hp->m, sizeof(FLOAT));
-	for (k = 0; k != hp->n; ++k)
-		for (b = 0; b != hp->m; ++b)
-			et[k][b] = hp->e[b][k];
-	// the initial state, drawn from a0[]
-	x = drand48();
-	for (k = 0, y = 0.0; k != hp->n; ++k) {
-		y += hp->a0[k];
-		if (y >= x) break;
-	}
-	// main loop
-	for (i = 0; i != L; ++i) {
-		FLOAT *el, *ak = hp->a[k];
-		x = drand48();
-		for (l = 0, y = 0.0; l != hp->n; ++l) {
-			y += ak[l];
-			if (y >= x) break;
-		}
-		el = et[l];
-		x = drand48();
-		for (b = 0, y = 0.0; b != hp->m; ++b) {
-			y += el[b];
-			if (y >= x) break;
-		} 
-		seq[i] = b;
-		k = l;
-	}
-	for (k = 0; k != hp->n; ++k) free(et[k]);
-	free(et);
-	return seq;
-}