filelist_t *get_filelist(const char *path, const char *filter) {
DIR *d;
struct stat st_in;
struct dirent *de, **names=0, **tmp;
size_t cnt=0, len=0;
filelist_t *filelist;
if (stat(path, &st_in) != 0 ) {
return NULL;
}
if (!S_ISDIR(st_in.st_mode)) {
filelist = filelist_alloc(1);
sprintf(filelist->files[0],"%s",path);
return filelist;
}
if ((d = opendir(path)) == NULL) {
return(NULL);
}
while ((de = readdir(d))) {
if (!file_selector(de->d_name, filter)) {
continue;
}
if (cnt >= len) {
len = 2*len+1;
if (len > SIZE_MAX/sizeof *names) {
break;
}
tmp = realloc(names, len * sizeof *names);
if (!tmp) {
break;
}
names = tmp;
}
names[cnt] = malloc(de->d_reclen);
if (!names[cnt]) {
break;
}
memcpy(names[cnt++], de, de->d_reclen);
}
closedir(d);
filelist = filelist_alloc(cnt);
if (names) {
while (cnt-->0) {
sprintf(filelist->files[cnt],"%s/%s",path,names[cnt]->d_name);
free(names[cnt]);
}
free(names);
}
return filelist;
}
filelist_t *MainWindow::QStringToFilelist(QFileInfoList list)
{
int i = 0;
filelist_t *fileList = filelist_alloc(list.size());
while (!list.isEmpty()) {
sprintf(fileList->files[i++],"%s",list.takeFirst().absoluteFilePath().toUtf8().data());
}
return fileList;
}
filelist_t *MainWindow::QStringToFilelist(QFileInfoList list)
{
int i = 0;
filelist_t *fileList = filelist_alloc(list.size());
while (!list.isEmpty()) {
sprintf(fileList->files[i++],"%s",list.takeFirst().absoluteFilePath().toUtf8().data());
if (is_filename_ascii(fileList->files[i-1]) == 0) {
QString message = tr("Unicode is not supported. Filenames must contain only ASCII characters. File: ") + fileList->files[i-1];
QMessageBox::critical(this, tr("Invalid Characters in filename"), message);
return NULL;
}
}
return fileList;
}
void MxfWriter::run()
{
int i = 0;
opendcpMxf->mxf.frame_done.callback = MxfWriter::frameDoneCb;
opendcpMxf->mxf.frame_done.argument = this;
filelist_t *fileList = filelist_alloc(mxfFileList.size());
while (!mxfFileList.isEmpty()) {
sprintf(fileList->files[i++],"%s",mxfFileList.takeFirst().absoluteFilePath().toUtf8().data());
}
rc = write_mxf(opendcpMxf, fileList, mxfOutputFile.toUtf8().data());
filelist_free(fileList);
emit setResult(rc);
emit finished();
}
filelist_t *get_filelist(const char *path, const char *filter) {
DIR *d;
struct stat st_in;
struct dirent *de;
char **names = 0, **tmp;
size_t cnt = 0, len = 0;
filelist_t *filelist;
if (stat(path, &st_in) != 0 ) {
OPENDCP_LOG(LOG_DEBUG, "path not found %s", path);
return NULL;
}
if (!S_ISDIR(st_in.st_mode)) {
OPENDCP_LOG(LOG_DEBUG, "single file mode");
filelist = filelist_alloc(1);
snprintf(filelist->files[0], MAX_FILENAME_LENGTH, "%s", path);
return filelist;
}
if ((d = opendir(path)) == NULL) {
return(NULL);
}
OPENDCP_LOG(LOG_DEBUG, "reading directory");
while ((de = readdir(d))) {
if (!file_selector(de->d_name, filter)) {
continue;
}
if (cnt >= len) {
len = 2 * len + 1;
if (len > SIZE_MAX / sizeof * names) {
break;
}
tmp = realloc(names, len * sizeof * names);
if (!tmp) {
break;
}
names = tmp;
}
names[cnt] = malloc(strlen(de->d_name) + 1);
if (!names[cnt]) {
break;
}
snprintf(names[cnt++], strlen(de->d_name) + 1, "%s", de->d_name);
OPENDCP_LOG(LOG_DEBUG, "Found %s", de->d_name);
}
closedir(d);
OPENDCP_LOG(LOG_DEBUG, "found %d files", cnt);
filelist = filelist_alloc(cnt);
if (names) {
while (cnt-- > 0) {
OPENDCP_LOG(LOG_DEBUG, "Adding file %s", names[cnt]);
snprintf(filelist->files[cnt], MAX_FILENAME_LENGTH, "%s/%s", path, names[cnt]);
free(names[cnt]);
}
free(names);
}
return filelist;
}
int main(int argc, char **argv)
{
if(argc < 3) print_usage(usage, NULL);
// Sample reads from ref
char *refpath = NULL;
// int optt = 0, tlen = 800; double tlen_stddev = 0.1;
int insert = 250, rlen = 250, single_ended = 0;
double depth = 1.0, insert_stddev_prop = 0.2; // stddev as proportion of insert
int optr = 0, opti = 0, optv = 0, optl = 0, optd = 0; // keeps track of values
uint64_t seed = generate_seed(); // default RNG seed
char *in0path = NULL, *in1path = NULL;
char *profile_paths[argc];
size_t num_profile_paths = 0, i, total_seq = 0;
float err_rate = -1;
int c;
while((c = getopt(argc, argv, "p:r:i:v:l:d:s1:2:e:g:")) >= 0) {
switch (c) {
case 'p': profile_paths[num_profile_paths++] = optarg; break;
case 'r': refpath = optarg; optr++; break;
// case 't': tlen = atoi(optarg); optt++; break;
// case 'v': tlen_stddev = atof(optarg); optv++; break;
case 'i': insert = atoi(optarg); opti++; break;
case 'v': insert_stddev_prop = atof(optarg); optv++; break;
case 'l': rlen = atoi(optarg); optl++; break;
case 'd': depth = atof(optarg); optd++; break;
case 's': single_ended = 1; break;
case '1': in0path = optarg; break;
case '2': in1path = optarg; break;
case 'e': err_rate = atof(optarg); break;
case 'g': seed = atoi(optarg); break;
default: die("Unknown option: %c", c);
}
}
// Set up
seed_random(seed);
init_qual_prob();
char *outbase = NULL;
if(optind == argc) {}//print_usage(usage, "Missing <out_base>");
else if(optind + 1 == argc) outbase = argv[optind];
else if(optind + 1 < argc) print_usage(usage, "Too many args after %s", outbase);
if(depth <= 0) print_usage(usage, "Depth [-d] cannot be <= 0");
if(insert_stddev_prop < 0)
print_usage(usage, "Insert length standard deviation [-v] cannot be < 0");
if((opti > 0 || optv > 0 || optl > 0 || optd > 0) && refpath == NULL)
print_usage(usage, "Missing -r <in.fa>");
if(optr > 1 || opti > 1 || optv > 1 || optl > 1 || optd > 1)
print_usage(usage, "Duplicate args");
if(in0path == NULL && in1path != NULL)
print_usage(usage, "-2 <in> requires -1 <in>");
if(in0path != NULL && in1path == NULL) {
if(refpath == NULL) single_ended = 1;
else if(!single_ended) print_usage(usage, "Missing -2 for paired-end output");
}
if(in0path != NULL && num_profile_paths == 0)
print_usage(usage, "Need at least one -p <profile.fq.gz> to use -1 .. -2 ..");
if(num_profile_paths == 0 && refpath == NULL)
print_usage(usage, "Need one of -p or -r");
if(num_profile_paths == 0 && outbase == NULL)
print_usage(usage, "More options required");
if(num_profile_paths > 0 && err_rate >= 0)
print_usage(usage, "Cannot use both -p and -E");
// Profile reads
FileList fliststore, *flist = NULL;
if(num_profile_paths > 0) {
flist = &fliststore;
filelist_alloc(flist, profile_paths, num_profile_paths);
}
if(outbase == NULL)
{
// Summarise error profile in input
filelist_mean_err(flist);
}
else
{
size_t outlen = strlen(outbase), extlen = strlen(".1.fa.gz");
char out0path[outlen+extlen+1], out1path[outlen+extlen+1];
memcpy(out0path, outbase, outlen);
memcpy(out1path, outbase, outlen);
if(single_ended) strcpy(out0path+outlen, ".fa.gz");
else {
strcpy(out0path+outlen, ".1.fa.gz");
strcpy(out1path+outlen, ".2.fa.gz");
}
gzFile gzout0 = NULL, gzout1 = NULL;
seq_file_t *sf0 = NULL, *sf1 = NULL, *reffile = NULL;
if(in0path != NULL && (sf0 = seq_open(in0path)) == NULL) die("Cannot read: %s", in0path);
if(in1path != NULL && (sf1 = seq_open(in1path)) == NULL) die("Cannot read: %s", in1path);
if(refpath != NULL)
{
if((reffile = seq_open(refpath)) == NULL) die("Cannot read: %s", refpath);
if((gzout0 = gzopen(out0path, "w")) == NULL) die("Cannot open: %s", out0path);
if(!single_ended && (gzout1 = gzopen(out1path, "w")) == NULL)
die("Cannot open: %s", out1path);
}
if(sf0 != NULL) {
printf("Adding error to input reads...\n");
total_seq += mutate_reads(sf0, gzout0, flist, err_rate);
seq_close(sf0);
}
if(sf1 != NULL) {
total_seq += mutate_reads(sf1, single_ended ? gzout0 : gzout1, flist, err_rate);
seq_close(sf1);
}
if(refpath != NULL)
{
printf("Sampling from %s\n", refpath);
printf(" sequencing depth: %.2f\n", depth);
printf(" read length: %i\n", rlen);
printf(" read pairs: %s\n", single_ended ? "no" : "yes");
if(!single_ended) {
printf(" insert length: %i\n", insert);
printf(" insert stddev: %.2f * insert = %.2f\n",
insert_stddev_prop, insert_stddev_prop*insert);
}
if(num_profile_paths > 0) {
printf(" seq error files: %s", flist->files[0]->path);
for(i = 1; i < num_profile_paths; i++)
printf(",%s", flist->files[i]->path);
printf("\n");
} else if(err_rate >= 0) {
printf(" seq error rate: %.2f%%\n", err_rate * 100.0);
} else {
printf(" sequencing errors: no\n");
}
total_seq += sim_reads(reffile, gzout0, gzout1, flist, err_rate,
insert, insert_stddev_prop*insert, rlen, depth);
seq_close(reffile);
}
if(gzout0 != NULL && gzout1 != NULL)
printf("Wrote %zu bases to: %s and %s\n", total_seq, out0path, out1path);
else if(gzout0 != NULL)
printf("Wrote %zu bases to: %s\n", total_seq, out0path);
if(gzout0 != NULL) gzclose(gzout0);
if(gzout1 != NULL) gzclose(gzout1);
}
if(flist != NULL)
{
// Print error distribution
size_t err_total = 0;
for(i = 0; i < flist->errors_len; i++) err_total += flist->errors[i];
printf("Errors: %zu / %zu (%.2f%%)\n", err_total, total_seq,
(100.0*err_total) / total_seq);
for(i = 0; i < flist->errors_len; i++) printf(" %zu", flist->errors[i]);
printf("\n");
filelist_dealloc(flist);
}
return EXIT_SUCCESS;
}
