int main(int argc, char *argv[]) {
int cmd_line_char, long_index;
struct files requiredFiles;
struct data taxInfo;
const struct option longopts[] = {
{"version", no_argument, 0, 'v'},
{"help", no_argument, 0, 'h'},
{"outfile", required_argument, 0, 'o'},
{"fastq", required_argument, 0, 'f'},
{"fixrank", required_argument, 0, 'r'},
{"tax_level", required_argument, 0, 'l'},
{"name", required_argument, 0, 'n',},
{0, 0, 0, 0}
};
while ((cmd_line_char = getopt_long(argc, argv, "vho:f:r:l:n:", longopts, &long_index)) != EOF) {
switch(cmd_line_char) {
case 'h':
printf("To use butter cup, please supply -o outputfile -f fastq file -r fixrank file and -l taxLevel -n tax Name\n");
printf("./Buttercup -o buttercup.out.fq -f <(zcat /mnt/home/alida/scratch/pplacer/vag_cancer/cancer.extendedFrags.fastq.gz) -r /mnt/home/alida/scratch/pplacer/vag_cancer/classify.fixrank -l genus -n Lactobacillus\n\n");
exit(0);
case 'o':
requiredFiles.outfile = fopen(optarg, "w");
if (requiredFiles.outfile == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'f':
requiredFiles.fastq = fopen(optarg, "r");
if (requiredFiles.fastq == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'r':
requiredFiles.fixrank = fopen(optarg, "r");
if (requiredFiles.fixrank == NULL) {
errorOut(&requiredFiles, &taxInfo);
}
break;
case 'l':
taxInfo.taxlevel = strdup(optarg);
break;
case 'n':
taxInfo.name = strdup(optarg);
break;
}
}
CreateSearchTree(&requiredFiles, &taxInfo);
return 0;
}
int main(int argc, char **argv) {
char *list_in;
char *file_out;
double ratio;
if (argc != 3 && argc != 4) {
printf("Usage: %s <list.txt> <outfile> [window_radius]\n", argv[0]);
return EXIT_FAILURE;
}
list_in = argv[1];
ratio = 0.6;
file_out = argv[2];
int window_radius = -1;
if (argc == 4) {
window_radius = atoi(argv[3]);
}
clock_t start = clock();
/* Read the list of files */
std::vector<std::string> key_files;
if (ReadFileList(list_in, key_files) != 0) return EXIT_FAILURE;
FILE *f;
if ((f = fopen(file_out, "w")) == NULL) {
printf("Could not open %s for writing.\n", file_out);
return EXIT_FAILURE;
}
int num_images = (int) key_files.size();
std::vector<unsigned char*> keys(num_images);
std::vector<int> num_keys(num_images);
/* Read all keys */
for (int i = 0; i < num_images; i++) {
keys[i] = NULL;
num_keys[i] = ReadKeyFile(key_files[i].c_str(), &keys[i]);
}
clock_t end = clock();
printf("[KeyMatchFull] Reading keys took %0.3fs\n",
(end - start) / ((double) CLOCKS_PER_SEC));
for (int i = 0; i < num_images; i++) {
if (num_keys[i] == 0)
continue;
printf("[KeyMatchFull] Matching to image %d\n", i);
start = clock();
/* Create a tree from the keys */
ANNkd_tree *tree = CreateSearchTree(num_keys[i], keys[i]);
/* Compute the start index */
int start_idx = 0;
if (window_radius > 0)
start_idx = std::max(i - window_radius, 0);
for (int j = start_idx; j < i; j++) {
if (num_keys[j] == 0)
continue;
/* Compute likely matches between two sets of keypoints */
std::vector<KeypointMatch> matches =
MatchKeys(num_keys[j], keys[j], tree, ratio);
int num_matches = (int) matches.size();
if (num_matches >= 16) {
/* Write the pair */
fprintf(f, "%d %d\n", j, i);
/* Write the number of matches */
fprintf(f, "%d\n", (int) matches.size());
for (int i = 0; i < num_matches; i++) {
fprintf(f, "%d %d\n",
matches[i].m_idx1, matches[i].m_idx2);
}
}
}
end = clock();
printf("[KeyMatchFull] Matching took %0.3fs\n",
(end - start) / ((double) CLOCKS_PER_SEC));
fflush(stdout);
delete tree;
}
/* Free keypoints */
for (int i = 0; i < num_images; i++) {
if (keys[i] != NULL)
delete [] keys[i];
}
fclose(f);
return EXIT_SUCCESS;
}
int main(int argc, char **argv) {
char *list_in;
char *file_out;
double ratio;
if (argc != 3) {
printf("Usage: %s <list.txt> <outfile>\n", argv[0]);
return -1;
}
list_in = argv[1];
ratio = 0.6;
file_out = argv[2];
clock_t start = clock();
unsigned char **keys;
int *num_keys;
/* Read the list of files */
std::vector<std::string> key_files;
FILE *f = fopen(list_in, "r");
if (f == NULL) {
printf("Error opening file %s for reading\n", list_in);
return 1;
}
char buf[512];
while (fgets(buf, 512, f)) {
/* Remove trailing newline */
if (buf[strlen(buf) - 1] == '\n')
buf[strlen(buf) - 1] = 0;
key_files.push_back(std::string(buf));
}
fclose(f);
f = fopen(file_out, "w");
assert(f != NULL);
int num_images = (int) key_files.size();
keys = new unsigned char *[num_images];
num_keys = new int[num_images];
/* Read all keys */
for (int i = 0; i < num_images; i++) {
keys[i] = NULL;
num_keys[i] = ReadKeyFile(key_files[i].c_str(), keys+i);
}
clock_t end = clock();
printf("[KeyMatchFull] Reading keys took %0.3fs\n",
(end - start) / ((double) CLOCKS_PER_SEC));
for (int i = 0; i < num_images; i++) {
if (num_keys[i] == 0)
continue;
printf("[KeyMatchFull] Matching to image %d\n", i);
start = clock();
/* Create a tree from the keys */
ANNkd_tree *tree = CreateSearchTree(num_keys[i], keys[i]);
for (int j = 0; j < i; j++) {
if (num_keys[j] == 0)
continue;
/* Compute likely matches between two sets of keypoints */
std::vector<KeypointMatch> matches =
MatchKeys(num_keys[j], keys[j], tree, ratio);
int num_matches = (int) matches.size();
if (num_matches >= 16) {
/* Write the pair */
fprintf(f, "%d %d\n", j, i);
/* Write the number of matches */
fprintf(f, "%d\n", (int) matches.size());
for (int i = 0; i < num_matches; i++) {
fprintf(f, "%d %d\n",
matches[i].m_idx1, matches[i].m_idx2);
}
}
}
end = clock();
printf("[KeyMatchFull] Matching took %0.3fs\n",
(end - start) / ((double) CLOCKS_PER_SEC));
fflush(stdout);
// annDeallocPts(tree->pts);
delete tree;
}
/* Free keypoints */
for (int i = 0; i < num_images; i++) {
if (keys[i] != NULL)
delete [] keys[i];
}
delete [] keys;
delete [] num_keys;
fclose(f);
return 0;
}
