/** * returns 0 on success, -1 on failure. */ int writeToFile(scram_fd* fp) { int r1 = scram_put_seq(fp, read1); if (r1 == 0 and isPaired()) { return scram_put_seq(fp, read2); } else { return r1; } }
int main(int argc, char **argv) { scram_fd **in, *out; int n_input, i; bam_seq_t **s; char imode[10], *in_f = "", omode[10], *out_f = ""; int level = '\0'; // nul terminate string => auto level int c, verbose = 0; int s_opt = 0, S_opt = 0, embed_ref = 0; char *ref_fn = NULL; int start, end; char ref_name[1024] = {0}; refs_t *refs = NULL; /* Parse command line arguments */ while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:XI:O:R:")) != -1) { switch (c) { case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': level = c; break; case 'u': level = '0'; break; case 'h': usage(stdout); return 0; case 'v': verbose++; break; case 's': s_opt = atoi(optarg); break; case 'S': S_opt = atoi(optarg); break; case 'V': cram_set_option(NULL, CRAM_OPT_VERSION, optarg); break; case 'r': ref_fn = optarg; break; case 'X': embed_ref = 1; break; case 'I': in_f = parse_format(optarg); break; case 'O': out_f = parse_format(optarg); break; case 'R': { char *cp = strchr(optarg, ':'); if (cp) { *cp = 0; switch (sscanf(cp+1, "%d-%d", &start, &end)) { case 1: end = start; break; case 2: break; default: fprintf(stderr, "Malformed range format\n"); return 1; } } else { start = INT_MIN; end = INT_MAX; } strncpy(ref_name, optarg, 1023); break; } case '?': fprintf(stderr, "Unrecognised option: -%c\n", optopt); usage(stderr); return 1; } } /* Open output file */ sprintf(omode, "w%s%c", out_f, level); if (!(out = scram_open("-", omode))) { fprintf(stderr, "Failed to open bam file %s\n", argv[optind+1]); return 1; } /* Open multiple input files */ sprintf(imode, "r%s%c", in_f, level); n_input = argc - optind; if (!n_input) { fprintf(stderr, "No input files specified.\n"); return 1; } if (!(in = malloc(n_input * sizeof(*in)))) return 1; if (!(s = malloc(n_input * sizeof(*s)))) return 1; for (i = 0; i < n_input; i++, optind++) { s[i] = NULL; if (*in_f == 0) sprintf(imode, "r%s%c", detect_format(argv[optind]), level); if (!(in[i] = scram_open(argv[optind], imode))) { fprintf(stderr, "Failed to open bam file %s\n", argv[optind]); return 1; } if (i && !hdr_compare(scram_get_header(in[0]), scram_get_header(in[i]))) { fprintf(stderr, "Incompatible reference sequence list.\n"); fprintf(stderr, "Currently the @SQ lines need to be identical" " in all files.\n"); return 1; } if (!refs && scram_get_refs(in[i])) refs = scram_get_refs(in[i]); if (refs && scram_set_option(in[i], CRAM_OPT_SHARED_REF, refs)) return 1; } /* Set any format specific options */ if (refs) scram_set_option(out, CRAM_OPT_SHARED_REF, refs); if (scram_set_option(out, CRAM_OPT_VERBOSITY, verbose)) return 1; if (s_opt) if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt)) return 1; if (S_opt) if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt)) return 1; if (embed_ref) if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref)) return 1; /* Copy header and refs from in to out, for writing purposes */ // FIXME: do proper merging of @PG lines // FIXME: track mapping of old PG aux name to new PG aux name per seq scram_set_header(out, sam_hdr_dup(scram_get_header(in[0]))); // Needs doing after loading the header. if (ref_fn) if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn)) return 1; if (scram_get_header(in[0])) { if (scram_write_header(out)) return 1; } /* Do the actual file format conversion */ fprintf(stderr, "Opening and loading initial seqs\n"); for (i = 0; i < n_input; i++) { if (scram_get_seq(in[i], &s[i]) < 0) { if (scram_close(in[i])) return 1; in[i] = NULL; free(s[i]); continue; } } fprintf(stderr, "Merging...\n"); for (;;) { int64_t best_val = INT64_MAX; int best_j = 0, j; for (j = 0; j < n_input; j++) { bam_seq_t *b = s[j]; uint64_t x; if (!in[j]) continue; x = (((uint64_t)bam_ref(b))<<33) | (bam_pos(b)<<2) | (bam_strand(b)<<1) | !(bam_flag(b) & BAM_FREAD1); if (best_val > x) { best_val = x; best_j = j; } } if (best_val == INT64_MAX) { // all closed break; } if (-1 == scram_put_seq(out, s[best_j])) return 1; if (scram_get_seq(in[best_j], &s[best_j]) < 0) { if (scram_close(in[best_j])) return 1; in[best_j] = NULL; free(s[best_j]); } } for (i = 0; i < n_input; i++) { if (!in[i]) continue; scram_close(in[i]); if (s[i]) free(s[i]); } /* Finally tidy up and close files */ if (scram_close(out)) return 1; free(in); free(s); return 0; }
int main(int argc, char **argv) { scram_fd *in, *out; bam_seq_t *s; char imode[10], *in_f = "", omode[10], *out_f = ""; int level = '\0'; // nul terminate string => auto level int c, verbose = 0; int s_opt = 0, S_opt = 0, embed_ref = 0, ignore_md5 = 0, decode_md = 0; char *ref_fn = NULL; int start, end, multi_seq = -1, no_ref = 0; int use_bz2 = 0, use_arith = 0, use_lzma = 0; char ref_name[1024] = {0}; refs_t *refs; int nthreads = 1; t_pool *p = NULL; int max_reads = -1; enum quality_binning binning = BINNING_NONE; /* Parse command line arguments */ while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:xXeI:O:R:!MmjJZt:BN:")) != -1) { switch (c) { case '0': case '1': case '2': case '3': case '4': case '5': case '6': case '7': case '8': case '9': level = c; break; case 'u': level = '0'; break; case 'h': usage(stdout); return 0; case 'v': verbose++; break; case 's': s_opt = atoi(optarg); break; case 'S': S_opt = atoi(optarg); break; case 'm': decode_md = 1; break; case 'V': if (cram_set_option(NULL, CRAM_OPT_VERSION, optarg)) return 1; break; case 'r': ref_fn = optarg; break; case 'X': fprintf(stderr, "-X is deprecated in favour of -e.\n"); case 'e': embed_ref = 1; break; case 'x': no_ref = 1; break; case 'I': in_f = parse_format(optarg); break; case 'O': out_f = parse_format(optarg); break; case 'R': { char *cp = strchr(optarg, ':'); if (cp) { *cp = 0; switch (sscanf(cp+1, "%d-%d", &start, &end)) { case 1: end = start; break; case 2: break; default: fprintf(stderr, "Malformed range format\n"); return 1; } } else { start = INT_MIN; end = INT_MAX; } strncpy(ref_name, optarg, 1023); break; } case '!': ignore_md5 = 1; break; case 'M': multi_seq = 1; break; case 'j': #ifdef HAVE_LIBBZ2 use_bz2 = 1; #else fprintf(stderr, "Warning: bzip2 support is not compiled into this" " version.\nPlease recompile.\n"); #endif break; case 'J': use_arith = 1; break; case 'Z': #ifdef HAVE_LIBLZMA use_lzma = 1; #else fprintf(stderr, "Warning: lzma support is not compiled into this" " version.\nPlease recompile.\n"); #endif break; case 't': nthreads = atoi(optarg); if (nthreads < 1) { fprintf(stderr, "Number of threads needs to be >= 1\n"); return 1; } break; case 'B': binning = BINNING_ILLUMINA; break; case 'N': // For debugging max_reads = atoi(optarg); break; case '?': fprintf(stderr, "Unrecognised option: -%c\n", optopt); usage(stderr); return 1; } } if (argc - optind > 2) { fprintf(stderr, "Usage: scramble [input_file [output_file]]\n"); return 1; } /* Open up input and output files */ sprintf(imode, "r%s%c", in_f, level); if (argc - optind > 0) { if (*in_f == 0) sprintf(imode, "r%s%c", detect_format(argv[optind]), level); if (!(in = scram_open(argv[optind], imode))) { fprintf(stderr, "Failed to open file %s\n", argv[optind]); return 1; } } else { if (!(in = scram_open("-", imode))) { fprintf(stderr, "Failed to open file %s\n", argv[optind]); return 1; } } if (!in->is_bam && ref_fn) { cram_load_reference(in->c, ref_fn); if (!in->c->refs && !embed_ref) { fprintf(stderr, "Unable to find an appropriate reference.\n" "Please specify a valid reference with " "-r ref.fa option.\n"); return 1; } } sprintf(omode, "w%s%c", out_f, level); if (argc - optind > 1) { if (*out_f == 0) sprintf(omode, "w%s%c", detect_format(argv[optind+1]), level); if (!(out = scram_open(argv[optind+1], omode))) { fprintf(stderr, "Failed to open file %s\n", argv[optind+1]); return 1; } } else { if (!(out = scram_open("-", omode))) { fprintf(stderr, "Failed to open file %s\n", argv[optind+1]); return 1; } } /* Set any format specific options */ scram_set_refs(out, refs = scram_get_refs(in)); scram_set_option(out, CRAM_OPT_VERBOSITY, verbose); if (s_opt) if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt)) return 1; if (S_opt) if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt)) return 1; if (embed_ref) if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref)) return 1; if (use_bz2) if (scram_set_option(out, CRAM_OPT_USE_BZIP2, use_bz2)) return 1; if (use_arith) if (scram_set_option(out, CRAM_OPT_USE_ARITH, use_arith)) return 1; if (use_lzma) if (scram_set_option(out, CRAM_OPT_USE_LZMA, use_lzma)) return 1; if (binning != BINNING_NONE) if (scram_set_option(out, CRAM_OPT_BINNING, binning)) return 1; if (no_ref) if (scram_set_option(out, CRAM_OPT_NO_REF, no_ref)) return 1; if (multi_seq) if (scram_set_option(out, CRAM_OPT_MULTI_SEQ_PER_SLICE, multi_seq)) return 1; if (decode_md) { if (no_ref) { fprintf(stderr, "Cannot use -m in conjunction with -x.\n"); return 1; } if (scram_set_option(in, CRAM_OPT_DECODE_MD, decode_md)) return 1; } if (nthreads > 1) { if (NULL == (p = t_pool_init(nthreads*2, nthreads))) return 1; if (scram_set_option(in, CRAM_OPT_THREAD_POOL, p)) return 1; if (scram_set_option(out, CRAM_OPT_THREAD_POOL, p)) return 1; } if (ignore_md5) if (scram_set_option(in, CRAM_OPT_IGNORE_MD5, ignore_md5)) return 1; /* Copy header and refs from in to out, for writing purposes */ scram_set_header(out, scram_get_header(in)); // Needs doing after loading the header. if (ref_fn) { if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn)) return 1; } else { // Attempt to fill out a cram->refs[] array from @SQ headers scram_set_option(out, CRAM_OPT_REFERENCE, NULL); } if (scram_get_header(out)) { char *arg_list = stringify_argv(argc, argv); if (!arg_list) return 1; if (sam_hdr_add_PG(scram_get_header(out), "scramble", "VN", PACKAGE_VERSION, "CL", arg_list, NULL)) return 1; if (scram_write_header(out)) return 1; free(arg_list); } /* Support for sub-range queries, currently implemented for CRAM only */ if (*ref_name != 0) { cram_range r; int refid; if (in->is_bam) { fprintf(stderr, "Currently the -R option is only implemented for CRAM indices\n"); return 1; } cram_index_load(in->c, argv[optind]); refid = sam_hdr_name2ref(in->c->header, ref_name); if (refid == -1 && *ref_name != '*') { fprintf(stderr, "Unknown reference name '%s'\n", ref_name); return 1; } r.refid = refid; r.start = start; r.end = end; if (scram_set_option(in, CRAM_OPT_RANGE, &r)) return 1; } /* Do the actual file format conversion */ s = NULL; while (scram_get_seq(in, &s) >= 0) { if (-1 == scram_put_seq(out, s)) { fprintf(stderr, "Failed to encode sequence\n"); return 1; } if (max_reads >= 0) if (--max_reads == 0) break; } if (max_reads == -1) { switch(scram_eof(in)) { case 0: fprintf(stderr, "Failed to decode sequence\n"); return 1; case 2: fprintf(stderr, "Warning: no end-of-file block identified. " "File may be truncated.\n"); break; case 1: default: // expected case break; } } /* Finally tidy up and close files */ if (scram_close(in)) return 1; if (scram_close(out)) return 1; if (p) t_pool_destroy(p, 0); if (s) free(s); return 0; }
// return 0 on success, -1 on failure int writeToFile(scram_fd* fp) { return scram_put_seq(fp, read); }