void
reorder
(
zerone_t * Z,
int * map
)
{
// NB: assume that r < 63 (checked by 'zerone()').
const unsigned int r = Z->ChIP->r;
const unsigned int n = nobs(Z->ChIP);
// Reorder 'Q'.
double Q[9] = {0};
for (int i = 0 ; i < 3 ; i++) {
for (int j = 0 ; j < 3 ; j++) {
Q[i+j*3] = Z->Q[map[i]+map[j]*3];
}
}
memcpy(Z->Q, Q, 9 * sizeof(double));
// Reorder 'p'.
double p[3*64] = {0};
for (int i = 0 ; i < 3 ; i++) {
for (int j = 0 ; j < r+1 ; j++) {
p[j+i*(r+1)] = Z->p[j+map[i]*(r+1)];
}
}
memcpy(Z->p, p, 3*(r+1) * sizeof(double));
// Reorder 'phi'.
double buffer[3] = {0};
for (int i = 0 ; i < n ; i++) {
for (int j = 0 ; j < 3 ; j++) buffer[j] = Z->phi[map[j]+i*3];
memcpy(Z->phi + 3*i, buffer, 3 * sizeof(double));
}
// Reorder 'pem'.
for (int i = 0 ; i < n ; i++) {
for (int j = 0 ; j < 3 ; j++) buffer[j] = Z->pem[map[j]+i*3];
memcpy(Z->pem + 3*i, buffer, 3 * sizeof(double));
}
return;
}
jahmm_t *
do_jahmm
(
ChIP_t *ChIP
)
{
// Extract the dimensions of the observations.
const unsigned int r = ChIP->r;
const unsigned int n = nobs(ChIP);
// Extract the first ChIP profile, which is the sum of
// negative controls.
int *ctrl = malloc(n * sizeof(int));
if (ctrl == NULL) {
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
return NULL;
}
for (size_t i = 0 ; i < n ; i++) {
ctrl[i] = ChIP->y[0+i*r];
}
zinb_par_t *z = mle_zinb(ctrl, n);
if (z == NULL) {
fprintf(stderr, "jahmm failure %s:%d\n", __FILE__, __LINE__);
apologize();
return NULL;
}
free(ctrl);
// Jahmm uses 3 states.
const unsigned int m = 3;
double *Q = malloc(m*m * sizeof(double));
double *p = malloc(m*(r+1) * sizeof(double));
if (Q == NULL || p == NULL) {
fprintf(stderr, "memory error: %s:%d\n", __FILE__, __LINE__);
return NULL;
}
// Set initial values of 'Q'.
for (size_t i = 0 ; i < m ; i++) {
for (size_t j = 0 ; j < m ; j++) {
Q[i+j*m] = (i==j) ? .95 : .05/(m-1);
}
}
// Set initial values of 'p'. The are not normalize, but the
// call to 'bw_zinm' will normalize them.
for (size_t i = 0 ; i < m ; i++) {
p[0+i*(r+1)] = z->p;
p[1+i*(r+1)] = 1 - z->p;
for (size_t j = 2 ; j < r+1 ; j++) {
p[j+i*(r+1)] = i + 0.5;
}
}
jahmm_t *jahmm = new_jahmm(m, ChIP);
if (jahmm == NULL) {
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
free(Q);
free(p);
return NULL;
}
set_jahmm_par(jahmm, Q, z->a, z->pi, p);
free(Q);
free(p);
Q = jahmm->Q;
p = jahmm->p;
// Run the Baum-Welch algorithm.
bw_zinm(jahmm);
// Reorder the states in case they got scrambled.
// We use the value of p0 as a sort key.
int tmp, map[3] = {0,1,2};
if (p[0*(r+1)] < p[1*(r+1)]) { tmp = map[0]; map[0] = map[1]; map[1] = tmp; }
if (p[1*(r+1)] < p[2*(r+1)]) { tmp = map[1]; map[1] = map[2]; map[2] = tmp; }
if (p[0*(r+1)] < p[1*(r+1)]) { tmp = map[0]; map[0] = map[1]; map[1] = tmp; }
if (map[0] != 0 || map[1] != 1) {
// The states have beem scrambled. We need to reorder
// 'Q', 'p', 'phi' and 'pem'.
double *phi = jahmm->phi;
double *pem = jahmm->pem;
double *Q_ = malloc(m*m * sizeof(double));
double *p_ = malloc(m*(r+1) * sizeof(double));
double *phi_ = malloc(m*n * sizeof(double));
double *pem_ = malloc(m*n * sizeof(double));
if (Q_ == NULL || p_ == NULL || phi_ == NULL || pem_ == NULL) {
// TODO: free everything
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
return NULL;
}
for (size_t j = 0 ; j < m ; j++) {
for (size_t i = 0 ; i < m ; i++) {
Q_[map[i]+map[j]*m] = Q[i+j*m];
}
}
memcpy(jahmm->Q, Q_, m*m * sizeof(double));
for (size_t j = 0 ; j < m ; j++) {
for (size_t i = 0 ; i < r+1 ; i++) {
p_[i+map[j]*(r+1)] = p[i+j*(r+1)];
}
}
memcpy(jahmm->p, p_, m*(r+1) * sizeof(double));
for (size_t j = 0 ; j < m ; j++) {
for (size_t i = 0 ; i < n ; i++) {
phi_[map[j]+i*m] = phi[j+i*m];
pem_[map[j]+i*m] = pem[j+i*m];
}
}
memcpy(jahmm->phi, phi_, m*n * sizeof(double));
memcpy(jahmm->pem, pem_, m*n * sizeof(double));
free(Q_);
free(p_);
free(phi_);
free(pem_);
}
// Run the Viterbi algorithm.
int *path = malloc(n * sizeof(int));
double *initp = malloc(m * sizeof(double));
double *log_Q = malloc(m*m * sizeof(double));
if (path == NULL || initp == NULL || log_Q == NULL) {
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
// TODO: free everything.
return NULL;
}
for (size_t i = 0 ; i < m ; i++) initp[i] = log(1.0/m);
for (size_t i = 0 ; i < m*m ; i++) log_Q[i] = log(Q[i]);
block_viterbi(m, ChIP->nb, ChIP->size, log_Q, initp, jahmm->pem, path);
jahmm->path = path;
free(initp);
free(log_Q);
return jahmm;
}
zerone_t *
do_zerone
(
ChIP_t * ChIP
)
{
// The number of state in Zerone is an important constant.
// So much depends on it that it may be frozen in the code.
const unsigned int m = 3;
int * mock = NULL; // The mock ChIP profile.
int * path = NULL; // The Viterbi path.
zinb_par_t * par = NULL; // The parameter estimates.
zerone_t * Z = NULL; // The Zerone instance.
// Extract the dimensions of the observations.
const unsigned int r = ChIP->r;
const unsigned int n = nobs(ChIP);
if (r > 63) {
fprintf(stderr, "maximum number of profiles exceeded\n");
goto clean_and_return;
}
// Extract the first ChIP profile (the sum of mock controls).
mock = malloc(n * sizeof(int));
if (mock == NULL) {
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
goto clean_and_return;
}
// Copy data to 'mock'.
for (size_t i = 0 ; i < n ; i++) {
mock[i] = ChIP->y[0+i*r];
}
par = mle_zinb(mock, n);
if (par == NULL) {
// TODO: Change parametrization so that failure does not happen. //
fprintf(stderr, "zerone failure %s:%d\n", __FILE__, __LINE__);
apologize();
goto clean_and_return;
}
free(mock);
mock = NULL;
double Q[9] = {0};
double p[3*64] = {0};
// Set initial values of 'Q'.
for (size_t i = 0 ; i < 3 ; i++) {
for (size_t j = 0 ; j < 3 ; j++) {
Q[i+j*3] = (i==j) ? .95 : .025;
}
}
// Set initial values of 'p'. They are not normalized,
// but the call to 'bw_zinm' will normalize them.
for (size_t i = 0 ; i < 3 ; i++) {
p[0+i*(r+1)] = par->p;
p[1+i*(r+1)] = 1 - par->p;
for (size_t j = 2 ; j < r+1 ; j++) {
p[j+i*(r+1)] = i + 0.5;
}
}
Z = new_zerone(3, ChIP);
if (Z == NULL) {
// TODO: handle this case properly. //
fprintf(stderr, "error in function '%s()' %s:%d\n",
__func__, __FILE__, __LINE__);
goto clean_and_return;
}
set_zerone_par(Z, Q, par->a, par->pi, p);
// Run the Baum-Welch algorithm.
bw_zinm(Z);
// Reorder the states in case they got scrambled.
// We use the value of p0 as a sort key (high p0
// means low average signal and vice versa).
int map[3] = {0,1,2};
for (int i = 1 ; i < 3 ; i++) {
if (Z->p[i*(r+1)] > Z->p[map[0]*(r+1)]) map[0] = i;
if (Z->p[(i-1)*(r+1)] < Z->p[map[2]*(r+1)]) map[2] = i-1;
}
// The middle state is the remaining one.
map[1] = 3-map[0]-map[2];
debug_print("map: [%d, %d, %d]\n", map[0], map[1], map[2]);
if (map[0] != 0 || map[1] != 1 || map[2] != 2) reorder(Z, map);
// Run the Viterbi algorithm.
double log_Q[9] = {0};
double initp[3] = {0};
path = malloc(n * sizeof(int));
if (path == NULL) {
fprintf(stderr, "memory error %s:%d\n", __FILE__, __LINE__);
goto clean_and_return;
}
for (size_t i = 0 ; i < 3 ; i++) initp[i] = log(1.0/3);
for (size_t i = 0 ; i < 9 ; i++) log_Q[i] = log(Z->Q[i]);
// Find Viterbi path.
block_viterbi(m, ChIP->nb, ChIP->sz, log_Q, initp, Z->pem, path);
Z->path = path;
clean_and_return:
// TODO: Do the cleaning if necessary. //
return Z;
}
int main(int argc, char **argv) {
debug_print("%s (DEBUG)\n", VERSION);
if (argc == 1) {
say_usage();
exit(EXIT_SUCCESS);
}
// Input file names (mock and ChIP).
char *mock_fnames[MAXNARGS+1] = {0};
char *ChIP_fnames[MAXNARGS+1] = {0};
int n_mock_files = 0;
int n_ChIP_files = 0;
int no_mock_specified = 1;
int no_ChIP_specified = 1;
static int list_flag = 0;
static int minmapq = 20;
static int window = 300;
static int mock_flag = 1;
static double minconf = 0.0;
// Needed to check 'strtoul()'.
char *endptr;
// Parse options.
debug_print("%s", "arguments:'\n");
while(1) {
int option_index = 0;
static struct option long_options[] = {
{"chip", required_argument, 0, '1'},
{"confidence", required_argument, 0, 'c'},
{"help", no_argument, 0, 'h'},
{"list-output", no_argument, &list_flag, 1 },
{"mock", required_argument, 0, '0'},
{"no-mock", no_argument, &mock_flag, 0 },
{"quality", required_argument, 0, 'q'},
{"version", no_argument, 0, 'v'},
{"window", required_argument, 0, 'w'},
{0, 0, 0, 0}
};
int c = getopt_long(argc, argv, "0:1:c:hlq:vw:",
long_options, &option_index);
// Done parsing named options. //
if (c == -1) break;
switch (c) {
case 0:
break;
case '0':
debug_print("| mock files(s): %s\n", optarg);
parse_fname(mock_fnames, optarg, &n_mock_files);
no_mock_specified = 0;
break;
case '1':
debug_print("| ChIP files(s): %s\n", optarg);
parse_fname(ChIP_fnames, optarg, &n_ChIP_files);
no_ChIP_specified = 0;
break;
case 'h':
say_usage();
return EXIT_SUCCESS;
case 'l':
list_flag = 1;
break;
case 'c':
// Decode argument with 'strtod()'
errno = 0;
endptr = NULL;
minconf = strtod(optarg, &endptr);
if (!check_strtoX(optarg, endptr) || minconf < 0 || minconf > 1) {
fprintf(stderr,
"zerone error: confidence must be "
"a float between 0 and 1\n");
say_usage();
return EXIT_FAILURE;
}
debug_print("| minconf: %f\n", minconf);
break;
case 'q':
// Decode argument with 'strtoul()'
errno = 0;
endptr = NULL;
minmapq = strtoul(optarg, &endptr, 10);
if (!check_strtoX(optarg, endptr) ||
minmapq < 0 || minmapq > 254) {
fprintf(stderr,
"zerone error: minimum mapping quality must be "
"an integer between 0 and 254\n");
say_usage();
return EXIT_FAILURE;
}
debug_print("| minmapq: %d\n", minmapq);
break;
case 'v':
say_version();
return EXIT_SUCCESS;
case 'w':
window = atoi(optarg);
if (window <= 0) {
fprintf(stderr, "zerone error: window must be a "
"positive integer\n");
say_usage();
return EXIT_FAILURE;
}
debug_print("| window: %d\n", window);
break;
default:
// Cannot parse. //
say_usage();
return EXIT_FAILURE;
}
}
// Now parse positional arguments (file names).
while (optind < argc) {
parse_fname(ChIP_fnames, argv[optind++], &n_ChIP_files);
}
debug_print("%s", "done parsing arguments\n");
// Check options.
if (no_mock_specified && mock_flag) {
fprintf(stderr,
"zerone error: specify a file for mock control experiment\n");
say_usage();
return EXIT_FAILURE;
}
if (no_ChIP_specified) {
fprintf(stderr,
"zerone error: specify a file for ChIP-seq experiment\n");
say_usage();
return EXIT_FAILURE;
}
// Process input files.
zerone_parser_args_t args;
args.window = window;
args.minmapq = minmapq;
ChIP_t *ChIP = parse_input_files(mock_fnames, ChIP_fnames, args);
if (ChIP == NULL) {
fprintf(stderr, "error while reading input\n");
exit(EXIT_FAILURE);
}
// debug info //
{
debug_print("%s", "done reading input files\n");
debug_print("%s", "ChIP:\n");
debug_print("| r = %ld (dimension)\n", ChIP->r);
debug_print("| nb = %d (block number)\n", ChIP->nb);
for (int j = 0 ; j < ChIP->nb ; j++) {
debug_print("| block %s (size: %d)\n",
ChIP->nm + 32*j, ChIP->sz[j]);
}
// Sum reads of all blocks.
size_t *nreads = calloc(ChIP->r, sizeof(size_t));
if (nreads == NULL) {
fprintf(stderr, "memory error\n");
exit(EXIT_FAILURE);
}
for (int i = 0 ; i < nobs(ChIP) ; i++) {
for (int j = 0 ; j < ChIP->r ; j++) {
nreads[j] += ChIP->y[j + i*ChIP->r];
}
}
debug_print("| aggregated mock: %ld reads\n", nreads[0]);
for (int j = 0 ; j < ChIP->r-1 ; j++) {
debug_print("| %s: %ld reads\n", ChIP_fnames[j], nreads[j+1]);
}
free(nreads);
}
// Do zerone.
debug_print("%s", "starting zerone\n");
zerone_t *Z = do_zerone(ChIP);
if (Z == NULL) {
fprintf(stderr, "run time error (sorry)\n");
exit(EXIT_FAILURE);
}
// debug info //
{
debug_print("%s", "Q:\n");
debug_print("%.3f %.3f %.3f\n", Z->Q[0], Z->Q[3], Z->Q[6]);
debug_print("%.3f %.3f %.3f\n", Z->Q[1], Z->Q[4], Z->Q[7]);
debug_print("%.3f %.3f %.3f\n", Z->Q[2], Z->Q[5], Z->Q[8]);
debug_print("%s", "p:\n");
for (int j = 0 ; j < 3 ; j++) {
int off = 0;
char debuf[512];
for (int i = 0 ; i < Z->r+1 ; i++) {
off += sprintf(debuf + off, "%.3f ", Z->p[i+j*(Z->r+1)]);
if (off > 499) break;
}
debug_print("%s\n", debuf);
}
}
// Quality control.
double feat[5];
double QC = zerone_qc(Z, feat);
fprintf(stdout, "# QC score: %.3f\n", QC);
fprintf(stdout, "# features: %.3f, %.3f, %.3f, %.3f, %.3f\n",
feat[0], feat[1], feat[2], feat[3], feat[4]);
fprintf(stdout, "# advice: %s discretization.\n",
QC >= 0 ? "accept" : "reject");
// List output.
if (list_flag) {
int wid = 0;
int target = 0;
double best = 0.0;
for (int i = 0 ; i < ChIP->nb ; i++) {
char *name = ChIP->nm + 32*i;
// Do not print the last bin because it may extend
// beyond the limit of the chromosome.
for (int j = 0 ; j < ChIP->sz[i]-1 ; j++) {
// Toggle on target state.
double conf = Z->phi[2+wid*3];
if (!target && Z->path[wid] == 2 && conf > minconf) {
fprintf(stdout, "%s\t%d\t", name, window*j + 1);
best = conf;
target = 1;
}
// Toggle off target state.
else if (target) {
// Update best score.
if (conf > best) best = conf;
if (Z->path[wid] != 2 || conf < minconf) {
fprintf(stdout, "%d\t%.5f\n", window*(j+1), best);
best = 0.0;
target = 0;
}
}
wid++;
}
// In case the end of the block is a target.
if (target) {
fprintf(stdout, "%d\t%.5f\n", window * ChIP->sz[i], best);
best = 0.0;
target = 0;
}
}
}
// Table output.
else {
// Use 'offset' to navigate in the ChIP blocks.
uint64_t offset = 0;
// In case no mock was provided, skip the column.
const int skipmock = mock_flag ? 0 : 1;
for (int i = 0 ; i < ChIP->nb ; i++) {
char *name = ChIP->nm + 32*i;
// Do not print the last bin because it may extend
// beyond the limit of the chromosome.
for (int j = 0 ; j < ChIP->sz[i]-1 ; j++) {
// Skip if 'confidence' too low.
if (Z->phi[2+(offset+j)*3] < minconf) continue;
fprintf(stdout, "%s\t%d\t%d\t%d", name, window*j + 1,
// Block name, window start, end, state.
window*(j+1), Z->path[offset+j] == 2 ? 1 : 0);
for (int k = skipmock ; k < Z->ChIP->r ; k++) {
fprintf(stdout, "\t%d",
// Read numbers of each file.
Z->ChIP->y[(offset+j)*Z->ChIP->r+k]);
}
fprintf(stdout, "\t%.5f\n",
// Confidence score.
Z->phi[2+(offset+j)*3]);
}
// End of the block. Update 'offset' before
// local window number is reset to 0.
offset += Z->ChIP->sz[i];
}
}
destroy_zerone_all(Z); // Also frees ChIP.
for (int i = 0 ; i < MAXNARGS ; i++) {
free(mock_fnames[i]);
free(ChIP_fnames[i]);
}
return 0;
}
