void nfs_cmn_err(int error, int level, char *fmt, ...) { va_list ap; char buf[FMT_BUF_SIZE]; /* massaged version of fmt */ /* Expand %m */ expand_format_string(error, fmt, buf, FMT_BUF_SIZE); /* * Now pass the massaged format string and its arguments off to * cmn_err. */ va_start(ap, fmt); (void) vzcmn_err(getzoneid(), level, buf, ap); va_end(ap); }
int main(int argc, char**argv) { // test state const int NUM_TESTS = 1; int verbose = 0; int success = 0; int failure = 0; int getopt_char; while ((getopt_char = getopt(argc, argv, "v")) != -1) { switch (getopt_char) { case 'v': ++verbose; break; default: printf( "usage: test_expand_format_string [-v]\n\n" " -v verbose output\n" ); break; } } // Setup pysamerr redirect kstring_t res = { 0, 0, NULL }; FILE* orig_pysamerr = fdopen(dup(STDERR_FILENO), "a"); // Save pysamerr char* tempfname = (optind < argc)? argv[optind] : "test_expand_format_string.tmp"; FILE* check = NULL; // setup if (verbose) printf("BEGIN test 1\n"); // default format string test const char* format_string_1 = "%*_%#.bam"; const char* basename_1 = "basename"; const char* rg_id_1 = "1#2.3"; const int rg_idx_1 = 4; if (verbose > 1) { printf("format_string:%s\n" "basename:%s\n" "rg_id:%s\n" "rg_idx:%d\n", format_string_1, basename_1, rg_id_1, rg_idx_1); } if (verbose) printf("RUN test 1\n"); // test xfreopen(tempfname, "w", pysamerr); // Redirect pysamerr to pipe char* output_1 = expand_format_string(format_string_1, basename_1, rg_id_1, rg_idx_1, NULL); fclose(pysamerr); if (verbose) printf("END RUN test 1\n"); if (verbose > 1) { printf("format_string:%s\n" "basename:%s\n" "rg_id:%s\n" "rg_idx:%d\n", format_string_1, basename_1, rg_id_1, rg_idx_1); } // check result res.l = 0; check = fopen(tempfname, "r"); if (output_1 != NULL && !strcmp(output_1, "basename_4.bam") && kgetline(&res, (kgets_func *)fgets, check) < 0 && (feof(check) || res.l == 0)) { ++success; } else { ++failure; if (verbose) printf("FAIL test 1\n"); } fclose(check); // teardown free(output_1); if (verbose) printf("END test 1\n"); // Cleanup test harness free(res.s); remove(tempfname); if (failure > 0) fprintf(orig_pysamerr, "%d failures %d successes\n", failure, success); fclose(orig_pysamerr); return (success == NUM_TESTS)? EXIT_SUCCESS : EXIT_FAILURE; }
// Set the initial state static state_t* init(parsed_opts_t* opts) { state_t* retval = calloc(sizeof(state_t), 1); if (!retval) { fprintf(pysamerr, "Out of memory"); return NULL; } retval->merged_input_file = sam_open(opts->merged_input_name, "rb"); if (!retval->merged_input_file) { fprintf(pysamerr, "Could not open input file (%s)\n", opts->merged_input_name); free(retval); return NULL; } retval->merged_input_header = sam_hdr_read(retval->merged_input_file); if (opts->unaccounted_name) { if (opts->unaccounted_header_name) { samFile* hdr_load = sam_open(opts->unaccounted_header_name, "r"); if (!hdr_load) { fprintf(pysamerr, "Could not open unaccounted header file (%s)\n", opts->unaccounted_header_name); cleanup_state(retval); return NULL; } retval->unaccounted_header = sam_hdr_read(hdr_load); sam_close(hdr_load); } else { retval->unaccounted_header = bam_hdr_dup(retval->merged_input_header); } retval->unaccounted_file = sam_open(opts->unaccounted_name, "wb"); if (retval->unaccounted_file == NULL) { fprintf(pysamerr, "Could not open unaccounted output file: %s\n", opts->unaccounted_name); cleanup_state(retval); return NULL; } } // Open output files for RGs if (!count_RG(retval->merged_input_header, &retval->output_count, &retval->rg_id)) return NULL; if (opts->verbose) fprintf(pysamerr, "@RG's found %zu\n",retval->output_count); retval->rg_output_file = (samFile**)calloc(retval->output_count, sizeof(samFile*)); retval->rg_output_header = (bam_hdr_t**)calloc(retval->output_count, sizeof(bam_hdr_t*)); retval->rg_hash = kh_init_c2i(); if (!retval->rg_output_file || !retval->rg_output_header) { fprintf(pysamerr, "Could not allocate memory for output file array. Out of memory?"); cleanup_state(retval); return NULL; } char* dirsep = strrchr(opts->merged_input_name, '/'); char* input_base_name = strdup(dirsep? dirsep+1 : opts->merged_input_name); if (!input_base_name) { fprintf(pysamerr, "Out of memory\n"); cleanup_state(retval); return NULL; } char* extension = strrchr(input_base_name, '.'); if (extension) *extension = '\0'; size_t i; for (i = 0; i < retval->output_count; i++) { char* output_filename = NULL; if ( ( output_filename = expand_format_string(opts->output_format_string, input_base_name, retval->rg_id[i], i) ) == NULL) { fprintf(pysamerr, "Error expanding output filename format string.\r\n"); cleanup_state(retval); free(input_base_name); return NULL; } retval->rg_output_file[i] = sam_open(output_filename, "wb"); if (retval->rg_output_file[i] == NULL) { fprintf(pysamerr, "Could not open output file: %s\r\n", output_filename); cleanup_state(retval); free(input_base_name); return NULL; } // Record index in hash int ret; khiter_t iter = kh_put_c2i(retval->rg_hash, retval->rg_id[i], &ret); kh_val(retval->rg_hash,iter) = i; // Set and edit header retval->rg_output_header[i] = bam_hdr_dup(retval->merged_input_header); if ( !filter_header_rg(retval->rg_output_header[i], retval->rg_id[i]) ) { fprintf(pysamerr, "Could not rewrite header for file: %s\r\n", output_filename); cleanup_state(retval); free(output_filename); free(input_base_name); return NULL; } free(output_filename); } free(input_base_name); return retval; }