void SampleRenderer::render_tile(CtxG&, Recti tile_rect,
Recti tile_film_rect, Film& tile_film, Sampler& sampler) const
{
StatTimer t(TIMER_RENDER_TILE);
Vec2 film_res(float(this->film->x_res), float(this->film->y_res));
for(int32_t y = tile_rect.p_min.y; y < tile_rect.p_max.y; ++y) {
for(int32_t x = tile_rect.p_min.x; x < tile_rect.p_max.x; ++x) {
sampler.start_pixel();
for(uint32_t s = 0; s < sampler.samples_per_pixel; ++s) {
sampler.start_pixel_sample();
Vec2 pixel_pos = sampler.get_sample_2d(this->pixel_pos_idx);
Vec2 film_pos = Vec2(float(x), float(y)) + pixel_pos;
Ray ray(this->scene->camera->cast_ray(film_res, film_pos));
Spectrum radiance = this->get_radiance(*this->scene, ray, 0, sampler);
assert(is_finite(radiance));
assert(is_nonnegative(radiance));
if(is_finite(radiance) && is_nonnegative(radiance)) {
Vec2 tile_film_pos = film_pos -
Vec2(float(tile_film_rect.p_min.x), float(tile_film_rect.p_min.y));
tile_film.add_sample(tile_film_pos, radiance);
}
}
}
}
}
void b2g_library_init(b2g_library_t *library, const char *name, b2g_cutoff_lminlmax_t *cutoff_lminlmax, int PROPER_LENGTH) {
assert(library && name && cutoff_lminlmax && is_nonnegative(PROPER_LENGTH));
b2g_library_stats_t stats = {PROPER_LENGTH, -1};
strcpy(library->name, name);
library->cutoff_lminlmax = *cutoff_lminlmax;
library->cutoff_data = stats;
}
/* process command-line arguments */
int
process_arguments (int argc, char **argv)
{
int c;
int option = 0;
static struct option longopts[] = {
{"hostname", required_argument, 0, 'H'},
{"query_address", required_argument, 0, 'l'},
{"warning", required_argument, 0, 'w'},
{"critical", required_argument, 0, 'c'},
{"timeout", required_argument, 0, 't'},
{"dig-arguments", required_argument, 0, 'A'},
{"verbose", no_argument, 0, 'v'},
{"version", no_argument, 0, 'V'},
{"help", no_argument, 0, 'h'},
{"record_type", required_argument, 0, 'T'},
{"expected_address", required_argument, 0, 'a'},
{"port", required_argument, 0, 'p'},
{"use-ipv4", no_argument, 0, '4'},
{"use-ipv6", no_argument, 0, '6'},
{0, 0, 0, 0}
};
if (argc < 2)
return ERROR;
while (1) {
c = getopt_long (argc, argv, "hVvt:l:H:w:c:T:p:a:A:46", longopts, &option);
if (c == -1 || c == EOF)
break;
switch (c) {
case 'h': /* help */
print_help ();
exit (STATE_UNKNOWN);
case 'V': /* version */
print_revision (progname, NP_VERSION);
exit (STATE_UNKNOWN);
case 'H': /* hostname */
host_or_die(optarg);
dns_server = optarg;
break;
case 'p': /* server port */
if (is_intpos (optarg)) {
server_port = atoi (optarg);
}
else {
usage_va(_("Port must be a positive integer - %s"), optarg);
}
break;
case 'l': /* address to lookup */
query_address = optarg;
break;
case 'w': /* warning */
if (is_nonnegative (optarg)) {
warning_interval = strtod (optarg, NULL);
}
else {
usage_va(_("Warning interval must be a positive integer - %s"), optarg);
}
break;
case 'c': /* critical */
if (is_nonnegative (optarg)) {
critical_interval = strtod (optarg, NULL);
}
else {
usage_va(_("Critical interval must be a positive integer - %s"), optarg);
}
break;
case 't': /* timeout */
if (is_intnonneg (optarg)) {
timeout_interval = atoi (optarg);
}
else {
usage_va(_("Timeout interval must be a positive integer - %s"), optarg);
}
break;
case 'A': /* dig arguments */
dig_args = strdup(optarg);
break;
case 'v': /* verbose */
verbose = TRUE;
break;
case 'T':
record_type = optarg;
break;
case 'a':
expected_address = optarg;
break;
case '4':
query_transport = "-4";
break;
case '6':
query_transport = "-6";
break;
default: /* usage5 */
usage5();
}
}
c = optind;
if (dns_server == NULL) {
if (c < argc) {
host_or_die(argv[c]);
dns_server = argv[c];
}
else {
if (strcmp(query_transport,"-6") == 0)
dns_server = strdup("::1");
else
dns_server = strdup ("127.0.0.1");
}
}
return validate_arguments ();
}
/* process command-line arguments */
int
process_arguments (int argc, char **argv)
{
int c;
char* temp;
int option = 0;
static struct option longopts[] = {
{"hostname", required_argument, 0, 'H'},
{"expect", required_argument, 0, 'e'},
{"critical", required_argument, 0, 'c'},
{"warning", required_argument, 0, 'w'},
{"timeout", required_argument, 0, 't'},
{"port", required_argument, 0, 'p'},
{"from", required_argument, 0, 'f'},
{"fqdn", required_argument, 0, 'F'},
{"authtype", required_argument, 0, 'A'},
{"authuser", required_argument, 0, 'U'},
{"authpass", required_argument, 0, 'P'},
{"command", required_argument, 0, 'C'},
{"response", required_argument, 0, 'R'},
{"verbose", no_argument, 0, 'v'},
{"version", no_argument, 0, 'V'},
{"use-ipv4", no_argument, 0, '4'},
{"use-ipv6", no_argument, 0, '6'},
{"help", no_argument, 0, 'h'},
{"starttls",no_argument,0,'S'},
{"certificate",required_argument,0,'D'},
{"ignore-quit-failure",no_argument,0,'q'},
{0, 0, 0, 0}
};
if (argc < 2)
return ERROR;
for (c = 1; c < argc; c++) {
if (strcmp ("-to", argv[c]) == 0)
strcpy (argv[c], "-t");
else if (strcmp ("-wt", argv[c]) == 0)
strcpy (argv[c], "-w");
else if (strcmp ("-ct", argv[c]) == 0)
strcpy (argv[c], "-c");
}
while (1) {
c = getopt_long (argc, argv, "+hVv46t:p:f:e:c:w:H:C:R:SD:F:A:U:P:q",
longopts, &option);
if (c == -1 || c == EOF)
break;
switch (c) {
case 'H': /* hostname */
if (is_host (optarg)) {
server_address = optarg;
}
else {
usage2 (_("Invalid hostname/address"), optarg);
}
break;
case 'p': /* port */
if (is_intpos (optarg))
server_port = atoi (optarg);
else
usage4 (_("Port must be a positive integer"));
break;
case 'F':
/* localhostname */
localhostname = strdup(optarg);
break;
case 'f': /* from argument */
from_arg = optarg + strspn(optarg, "<");
from_arg = strndup(from_arg, strcspn(from_arg, ">"));
send_mail_from = 1;
break;
case 'A':
authtype = optarg;
use_ehlo = TRUE;
break;
case 'U':
authuser = optarg;
break;
case 'P':
authpass = optarg;
break;
case 'e': /* server expect string on 220 */
server_expect = optarg;
break;
case 'C': /* commands */
if (ncommands >= command_size) {
command_size+=8;
commands = realloc (commands, sizeof(char *) * command_size);
if (commands == NULL)
die (STATE_UNKNOWN,
_("Could not realloc() units [%d]\n"), ncommands);
}
commands[ncommands] = (char *) malloc (sizeof(char) * 255);
strncpy (commands[ncommands], optarg, 255);
ncommands++;
break;
case 'R': /* server responses */
if (nresponses >= response_size) {
response_size += 8;
responses = realloc (responses, sizeof(char *) * response_size);
if (responses == NULL)
die (STATE_UNKNOWN,
_("Could not realloc() units [%d]\n"), nresponses);
}
responses[nresponses] = (char *) malloc (sizeof(char) * 255);
strncpy (responses[nresponses], optarg, 255);
nresponses++;
break;
case 'c': /* critical time threshold */
if (!is_nonnegative (optarg))
usage4 (_("Critical time must be a positive"));
else {
critical_time = strtod (optarg, NULL);
check_critical_time = TRUE;
}
break;
case 'w': /* warning time threshold */
if (!is_nonnegative (optarg))
usage4 (_("Warning time must be a positive"));
else {
warning_time = strtod (optarg, NULL);
check_warning_time = TRUE;
}
break;
case 'v': /* verbose */
verbose++;
break;
case 'q':
ignore_send_quit_failure++; /* ignore problem sending QUIT */
break;
case 't': /* timeout */
if (is_intnonneg (optarg)) {
socket_timeout = atoi (optarg);
}
else {
usage4 (_("Timeout interval must be a positive integer"));
}
break;
case 'S':
/* starttls */
use_ssl = TRUE;
use_ehlo = TRUE;
break;
case 'D':
/* Check SSL cert validity */
#ifdef USE_OPENSSL
if ((temp=strchr(optarg,','))!=NULL) {
*temp='\0';
if (!is_intnonneg (optarg))
usage2 ("Invalid certificate expiration period", optarg);
days_till_exp_warn = atoi(optarg);
*temp=',';
temp++;
if (!is_intnonneg (temp))
usage2 (_("Invalid certificate expiration period"), temp);
days_till_exp_crit = atoi (temp);
}
else {
days_till_exp_crit=0;
if (!is_intnonneg (optarg))
usage2 ("Invalid certificate expiration period", optarg);
days_till_exp_warn = atoi (optarg);
}
check_cert = TRUE;
#else
usage (_("SSL support not available - install OpenSSL and recompile"));
#endif
break;
case '4':
address_family = AF_INET;
break;
case '6':
#ifdef USE_IPV6
address_family = AF_INET6;
#else
usage4 (_("IPv6 support not available"));
#endif
break;
case 'V': /* version */
print_revision (progname, NP_VERSION);
exit (STATE_OK);
case 'h': /* help */
print_help ();
exit (STATE_OK);
case '?': /* help */
usage5 ();
}
}
c = optind;
if (server_address == NULL) {
if (argv[c]) {
if (is_host (argv[c]))
server_address = argv[c];
else
usage2 (_("Invalid hostname/address"), argv[c]);
}
else {
xasprintf (&server_address, "127.0.0.1");
}
}
if (server_expect == NULL)
server_expect = strdup (SMTP_EXPECT);
if (mail_command == NULL)
mail_command = strdup("MAIL ");
if (from_arg==NULL)
from_arg = strdup(" ");
return validate_arguments ();
}
/* process command-line arguments */
int
process_arguments (int argc, char **argv)
{
int c;
int option = 0;
static struct option longopts[] = {
{"help", no_argument, 0, 'h'},
{"version", no_argument, 0, 'V'},
{"timeout", required_argument, 0, 't'},
{"critical", required_argument, 0, 'c'},
{"warning", required_argument, 0, 'w'},
{"hostname", required_argument, 0, 'H'},
{"logname", required_argument, 0, 'l'},
{"password", required_argument, 0, 'p'},
{"authorization", required_argument, 0, 'a'},
{"port", required_argument, 0, 'P'},
{"database", required_argument, 0, 'd'},
{"verbose", no_argument, 0, 'v'},
{0, 0, 0, 0}
};
while (1) {
c = getopt_long (argc, argv, "hVt:c:w:H:P:d:l:p:a:v",
longopts, &option);
if (c == EOF)
break;
switch (c) {
case '?': /* usage */
usage5 ();
case 'h': /* help */
print_help ();
exit (STATE_OK);
case 'V': /* version */
print_revision (progname, NP_VERSION);
exit (STATE_OK);
case 't': /* timeout period */
if (!is_integer (optarg))
usage2 (_("Timeout interval must be a positive integer"), optarg);
else
timeout_interval = atoi (optarg);
break;
case 'c': /* critical time threshold */
if (!is_nonnegative (optarg))
usage2 (_("Critical threshold must be a positive integer"), optarg);
else
tcrit = strtod (optarg, NULL);
break;
case 'w': /* warning time threshold */
if (!is_nonnegative (optarg))
usage2 (_("Warning threshold must be a positive integer"), optarg);
else
twarn = strtod (optarg, NULL);
break;
case 'H': /* host */
if (!is_host (optarg))
usage2 (_("Invalid hostname/address"), optarg);
else
pghost = optarg;
break;
case 'P': /* port */
if (!is_integer (optarg))
usage2 (_("Port must be a positive integer"), optarg);
else
pgport = optarg;
break;
case 'd': /* database name */
if (!is_pg_dbname (optarg)) /* checks length and valid chars */
usage2 (_("Database name is not valid"), optarg);
else /* we know length, and know optarg is terminated, so us strcpy */
strcpy (dbName, optarg);
break;
case 'l': /* login name */
if (!is_pg_logname (optarg))
usage2 (_("User name is not valid"), optarg);
else
pguser = optarg;
break;
case 'p': /* authentication password */
case 'a':
pgpasswd = optarg;
break;
case 'v':
verbose++;
break;
}
}
return validate_arguments ();
}
inline bool is_nonnegative(const RgbSpectrum& s) {
return is_nonnegative(s.rgb);
}
// num_skipped counts the number of reads that do not show up in output. Used by validate to account for all the input reads.
b2g_error_t params2gasv_input(char *BAM_PATH, char *OUTPUT_PREFIX, int MAPPING_QUALITY, int WRITE_CONCORDANT, int WRITE_LOWQ, int LOW_MEMORY, int AMBIGUOUS, int LIB_SEP, int VERBOSE, int CUTOFF_X, int CUTOFF_Y, b2g_cutoff_lminlmax_mode_t CUTOFF_MODE, char *CUTOFF_NAME, int PROPER_LENGTH, int USE_NUMBER_READS, int DEBUG_LEVEL, int WRITE_SPLITREAD, int MIN_ALIGNED_PCT, char *CHROMOSOME_NAMING, b2g_platform_t PLATFORM, int VALIDATION_STRINGENCY, int GASV_PRO, int IGNORE_DUPLICATES, int QNAME_SORTED, int SPLIT_BY_CHROMOSOME, unsigned int *num_skipped) {
assert(BAM_PATH && OUTPUT_PREFIX && in_range(MAPPING_QUALITY, 0, 255) && is_bool(WRITE_CONCORDANT) && is_bool(WRITE_LOWQ) && is_bool(LOW_MEMORY) && is_bool(AMBIGUOUS) && is_bool(LIB_SEP) && is_bool(VERBOSE) && CUTOFF_MODE && (FILENAME != CUTOFF_MODE || CUTOFF_NAME) && is_nonnegative(PROPER_LENGTH) && is_positive(USE_NUMBER_READS) && is_bool(WRITE_SPLITREAD) && in_range(MIN_ALIGNED_PCT, 50, 100) && is_bool(GASV_PRO) && is_bool(IGNORE_DUPLICATES) && is_bool(SPLIT_BY_CHROMOSOME));
b2g_error_t ERR = B2GERR_NO_ERROR;
hash_t *pairtable = NULL;
samfile_t *in = NULL, *lowq_file = NULL, *split_file = NULL;
FILE *chromosome_naming_file = NULL, *cutoff_file = NULL, *info_file = NULL, *gasv_file = NULL, *gasvpro_file = NULL;
unsigned long GENOME_LENGTH = DEFAULT_GENOME_LENGTH;
if (GASV_PRO && !WRITE_CONCORDANT) {
if (VERBOSE) printf("-WRITE_CONCORDANT is required for -GASVPRO output. Automatically enabling.\n\n");
WRITE_CONCORDANT = 1;
}
if (AMBIGUOUS && !QNAME_SORTED) {
if (VERBOSE) printf("-QNAME_SORTED is required for -AMBIGUOUS output. Automatically enabling.\n\n");
QNAME_SORTED = 1;
}
if (FILENAME == CUTOFF_MODE && !LIB_SEP) {
if (VERBOSE) printf("-LIB_SEP sep is required for -CUTOFF_LMINLMAX FILE=... output. Automatically enabling.\n\n");
LIB_SEP = 1;
}
if (AMBIGUOUS && (WRITE_LOWQ || WRITE_SPLITREAD)) {
if (VERBOSE) printf("-WRITE_LOWQ and -WRITE_SPLITREAD behavior are undefined for -AMBIGUOUS. Automatically disabling\n\n");
WRITE_LOWQ = WRITE_SPLITREAD = 0;
}
// Open all external resources and abort if failure.
if ((ERR = _open_files(&in, &chromosome_naming_file, &cutoff_file, &lowq_file, &split_file, &info_file, &gasv_file, &gasvpro_file, BAM_PATH, OUTPUT_PREFIX, CHROMOSOME_NAMING, CUTOFF_MODE, CUTOFF_NAME, WRITE_LOWQ, WRITE_SPLITREAD, GASV_PRO))) return _cleanup(in, chromosome_naming_file, cutoff_file, lowq_file, split_file, info_file, gasv_file, gasvpro_file, pairtable, ERR);
// Allocate hash table
struct stat st;
stat(BAM_PATH, &st);
if (!(pairtable = hash(!QNAME_SORTED * ((st.st_size / B2G_HASH_SIZE) / (LOW_MEMORY ? MAX_BAM_FILES : 1))))) return _cleanup(in, chromosome_naming_file, cutoff_file, lowq_file, split_file, info_file, gasv_file, gasvpro_file, pairtable, B2GERR_OUT_OF_MEMORY);
// Calculate required space for bam_header metadata,
int NUM_CHROMOSOMES, NUM_READGROUPS, NUM_LIBRARIES;
b2g_bam_header_counts(in->header, &NUM_CHROMOSOMES, &NUM_READGROUPS, &NUM_LIBRARIES, &LIB_SEP, PROPER_LENGTH);
// allocate memory for said data,
b2g_cutoff_lminlmax_t cutoff_lminlmax = {CUTOFF_MODE, CUTOFF_X , CUTOFF_Y, CUTOFF_NAME};
int chromosome_numbers[NUM_CHROMOSOMES];
b2g_chromosomes_t chromosomes = {NUM_CHROMOSOMES, chromosome_numbers};
b2g_readgroup2library_t rgs2libs[NUM_READGROUPS];
b2g_library_t libs[NUM_LIBRARIES];
b2g_libraries_t libraries = {NUM_READGROUPS, NUM_LIBRARIES, &rgs2libs[0], &libs[0]};
// and read the header into that memory.
if ((ERR = b2g_bam_header_read(in->header, &chromosomes, &libraries, &GENOME_LENGTH, cutoff_lminlmax, chromosome_naming_file, cutoff_file, LIB_SEP, USE_NUMBER_READS, PROPER_LENGTH, VERBOSE))) return _cleanup(in, chromosome_naming_file, cutoff_file, lowq_file, split_file, info_file, gasv_file, gasvpro_file, pairtable, ERR);
// Do all the main program logic of splitting the bam file, sorting the contents, merging the final output, and dumping the statistics.
if ((ERR = _split_sort_merge_dump(BAM_PATH, OUTPUT_PREFIX, MAPPING_QUALITY, WRITE_CONCORDANT, WRITE_LOWQ, LOW_MEMORY, AMBIGUOUS, LIB_SEP, VERBOSE, CUTOFF_X, CUTOFF_Y, CUTOFF_MODE, CUTOFF_NAME, PROPER_LENGTH, USE_NUMBER_READS, DEBUG_LEVEL, WRITE_SPLITREAD, MIN_ALIGNED_PCT, CHROMOSOME_NAMING, PLATFORM, GASV_PRO, IGNORE_DUPLICATES, lowq_file, split_file, &libraries, &chromosomes, pairtable, info_file, gasv_file, gasvpro_file, GENOME_LENGTH, QNAME_SORTED, SPLIT_BY_CHROMOSOME, num_skipped))) return _cleanup(in, chromosome_naming_file, cutoff_file, lowq_file, split_file, info_file, gasv_file, gasvpro_file, pairtable, ERR);
return _cleanup(in, chromosome_naming_file, cutoff_file, lowq_file, split_file, info_file, gasv_file, gasvpro_file, pairtable, B2GERR_NO_ERROR);
}
