/* htsfile.c -- file identifier and minimal viewer. Copyright (C) 2014-2018 Genome Research Ltd. Author: John Marshall Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include #include #include #include #include #include #include #include #include #include "htslib/hfile.h" #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/vcf.h" enum { identify, view_headers, view_all } mode = identify; int show_headers = 1; int verbose = 0; int status = EXIT_SUCCESS; /* Exit status from main */ void error(const char *format, ...) { int err = errno; va_list args; va_start(args, format); fflush(stdout); fprintf(stderr, "htsfile: "); vfprintf(stderr, format, args); if (err) fprintf(stderr, ": %s\n", strerror(err)); else fprintf(stderr, "\n"); fflush(stderr); va_end(args); status = EXIT_FAILURE; } static htsFile *dup_stdout(const char *mode) { int fd = dup(STDOUT_FILENO); hFILE *hfp = (fd >= 0)? hdopen(fd, mode) : NULL; return hfp? hts_hopen(hfp, "-", mode) : NULL; } static void view_sam(samFile *in, const char *filename) { bam1_t *b = NULL; bam_hdr_t *hdr = NULL; samFile *out = NULL; hdr = sam_hdr_read(in); if (hdr == NULL) { errno = 0; error("reading headers from \"%s\" failed", filename); goto clean; } out = dup_stdout("w"); if (out == NULL) { error("reopening standard output failed"); goto clean; } if (show_headers) { if (sam_hdr_write(out, hdr) != 0) { error("writing headers to standard output failed"); goto clean; } } if (mode == view_all) { int ret; b = bam_init1(); if (b == NULL) { error("can't create record"); goto clean; } while ((ret = sam_read1(in, hdr, b)) >= 0) { if (sam_write1(out, hdr, b) < 0) { error("writing to standard output failed"); goto clean; } } if (ret < -1) { error("reading \"%s\" failed", filename); goto clean; } } clean: bam_hdr_destroy(hdr); bam_destroy1(b); if (out) hts_close(out); } static void view_vcf(vcfFile *in, const char *filename) { bcf1_t *rec = NULL; bcf_hdr_t *hdr = NULL; vcfFile *out = NULL; hdr = bcf_hdr_read(in); if (hdr == NULL) { errno = 0; error("reading headers from \"%s\" failed", filename); goto clean; } out = dup_stdout("w"); if (out == NULL) { error("reopening standard output failed"); goto clean; } if (show_headers) { if (bcf_hdr_write(out, hdr) != 0) { error("writing headers to standard output failed"); goto clean; } } if (mode == view_all) { int ret; rec = bcf_init(); if (rec == NULL) { error("can't create record"); goto clean; } while ((ret = bcf_read(in, hdr, rec)) >= 0) { if (bcf_write(out, hdr, rec) < 0) { error("writing to standard output failed"); goto clean; } } if (ret < -1) { error("reading \"%s\" failed", filename); goto clean; } } clean: if (hdr) bcf_hdr_destroy(hdr); if (rec) bcf_destroy(rec); if (out) hts_close(out); } static void view_raw(hFILE *fp, const char *filename) { int c, prev; for (prev = '\n'; (c = hgetc(fp)) != EOF; prev = c) if (isprint(c) || c == '\n' || c == '\t') putchar(c); else if (c == '\r') fputs("\\r", stdout); else if (c == '\0') fputs("\\0", stdout); else printf("\\x%02x", c); if (prev != '\n') putchar('\n'); if (herrno(fp)) { errno = herrno(fp); error("reading \"%s\" failed", filename); } } static void usage(FILE *fp, int status) { fprintf(fp, "Usage: htsfile [-chHv] FILE...\n" "Options:\n" " -c, --view Write textual form of FILEs to standard output\n" " -h, --header-only Display only headers in view mode, not records\n" " -H, --no-header Suppress header display in view mode\n" " -v, --verbose Increase verbosity of warnings and diagnostics\n"); exit(status); } int main(int argc, char **argv) { static const struct option options[] = { { "header-only", no_argument, NULL, 'h' }, { "no-header", no_argument, NULL, 'H' }, { "view", no_argument, NULL, 'c' }, { "verbose", no_argument, NULL, 'v' }, { "help", no_argument, NULL, '?' }, { "version", no_argument, NULL, 1 }, { NULL, 0, NULL, 0 } }; int c, i; status = EXIT_SUCCESS; while ((c = getopt_long(argc, argv, "chHv?", options, NULL)) >= 0) switch (c) { case 'c': mode = view_all; break; case 'h': mode = view_headers; show_headers = 1; break; case 'H': show_headers = 0; break; case 'v': hts_verbose++; verbose++; break; case 1: printf( "htsfile (htslib) %s\n" "Copyright (C) 2018 Genome Research Ltd.\n", hts_version()); exit(EXIT_SUCCESS); break; case '?': usage(stdout, EXIT_SUCCESS); break; default: usage(stderr, EXIT_FAILURE); break; } if (optind == argc) usage(stderr, EXIT_FAILURE); for (i = optind; i < argc; i++) { hFILE *fp = hopen(argv[i], "r"); if (fp == NULL) { error("can't open \"%s\"", argv[i]); continue; } if (mode == identify) { htsFormat fmt; if (hts_detect_format(fp, &fmt) < 0) { error("detecting \"%s\" format failed", argv[i]); hclose_abruptly(fp); continue; } char *description = hts_format_description(&fmt); printf("%s:\t%s\n", argv[i], description); free(description); } else { htsFile *hts = hts_hopen(fp, argv[i], "r"); if (hts) { switch (hts_get_format(hts)->category) { case sequence_data: view_sam(hts, argv[i]); break; case variant_data: view_vcf(hts, argv[i]); break; default: if (verbose) view_raw(fp, argv[i]); else { errno = 0; error("can't view \"%s\": unknown format", argv[i]); } break; } if (hts_close(hts) < 0) error("closing \"%s\" failed", argv[i]); fp = NULL; } else if (errno == ENOEXEC && verbose) view_raw(fp, argv[i]); else error("can't view \"%s\"", argv[i]); } if (fp && hclose(fp) < 0) error("closing \"%s\" failed", argv[i]); } return status; }