diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/c/multifasta_to_otu.c | 38 |
1 files changed, 29 insertions, 9 deletions
diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index 3c4850b..afc1397 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -45,7 +45,7 @@ void usage() { " print version.\n"); } -char **get_fasta_files_from_file(char *fn) { +char **get_fasta_files_from_file(char *fn, int file_override) { char **files; int files_count = 0; @@ -68,7 +68,7 @@ char **get_fasta_files_from_file(char *fn) { strncpy(file, line, strlen(line) + 1 ); file[strlen(file)- 1] = '\0'; - if(access(file, F_OK) == 0) { + if(access(file, F_OK) == 0 || file_override) { files[files_count] = file; files_count++; @@ -171,6 +171,7 @@ int main(int argc, char **argv) { char *input_fasta_directory = NULL; char *input_fasta_filelist = NULL; + char *input_fasta_filenamelist = NULL; char *sensing_matrix_filename = NULL; char *output_filename = NULL; @@ -202,6 +203,7 @@ int main(int argc, char **argv) { static struct option long_options[] = { {"input-directory", required_argument, 0, 'i'}, {"input-filelist", required_argument, 0, 'f'}, + {"input-filename-list", required_argument, 0, 'n'}, {"kmer", required_argument, 0, 'k'}, {"lambda", required_argument, 0, 'l'}, {"jobs", required_argument, 0, 'j'}, @@ -217,7 +219,7 @@ int main(int argc, char **argv) { while (1) { int option_index = 0; - c = getopt_long (argc, argv, "f:k:l:s:i:o:j:r:hvV", long_options, &option_index); + c = getopt_long (argc, argv, "f:k:l:s:i:o:n:j:r:hvV", long_options, &option_index); if (c == -1) break; @@ -229,6 +231,10 @@ int main(int argc, char **argv) { case 'f': input_fasta_filelist = optarg; break; + case 'n': + printf("using -n\n"); + input_fasta_filenamelist = optarg; + break; case 'j': jobs = atoi(optarg); break; @@ -318,10 +324,16 @@ int main(int argc, char **argv) { // load filenames char **filenames = NULL; - if(input_fasta_directory != NULL) + char **filenames_alternative = NULL; + if(input_fasta_directory != NULL) { filenames = get_fasta_files_from_directory(input_fasta_directory); - else - filenames = get_fasta_files_from_file(input_fasta_filelist); + } + else { + filenames = get_fasta_files_from_file(input_fasta_filelist, 0); + if(input_fasta_filenamelist != NULL) { + filenames_alternative = get_fasta_files_from_file(input_fasta_filenamelist, 1); + } + } while(filenames[dir_count] != NULL) dir_count++; @@ -356,7 +368,7 @@ int main(int argc, char **argv) { printf("Beginning to process samples\n"); - #pragma omp parallel for shared(solutions, sensing_matrix_ptr, done) + //#pragma omp parallel for shared(solutions, sensing_matrix_ptr, done) for(size_t i = 0; i < dir_count; i++ ) { size_t x = 0; @@ -469,10 +481,18 @@ int main(int argc, char **argv) { fprintf(output_fh, "#OTU_ID\t"); // print our filename headers + + char **filename_array_to_use = filenames; + if(filenames_alternative != NULL) { + printf("using alternative: %s %s\n", filenames_alternative[0], filenames[0]); + filename_array_to_use = filenames_alternative; + printf("using alternative: %s %s\n", filenames_alternative[0], filenames[0]); + } + for(i = 0; i < dir_count - 1; i++) { - fprintf(output_fh, "%s\t", basename(filenames[i])); + fprintf(output_fh, "%s\t", basename(filename_array_to_use[i])); } - fprintf(output_fh, "%s\n", basename(filenames[dir_count - 1])); + fprintf(output_fh, "%s\n", basename(filename_array_to_use[dir_count - 1])); for(j = 0; j < sequences; j++) { |