7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/htsfile.c src/htslib/htsfile.c deleted file mode 100644 index bfd0a748911..00000000000 --- src/htslib/htsfile.c +++ /dev/null @@ -1,234 +0,0 @@ -/* htsfile.c -- file identifier and minimal viewer. - - Copyright (C) 2014-2015 Genome Research Ltd. - - Author: John Marshall <jm18@sanger.ac.uk> - -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 <config.h> - -#include <errno.h> -#include <stdio.h> -#include <stdlib.h> -#include <getopt.h> -#include <unistd.h> - -#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 status = EXIT_SUCCESS; /* Exit status from main */ - -static htsFile *dup_stdout(const char *mode) -{ - int fd = dup(STDOUT_FILENO); - if (fd < 0) { - perror("htsfile: Couldn't duplicate stdout"); - return NULL; - } - hFILE *hfp = hdopen(fd, mode); - return hfp? hts_hopen(hfp, "-", mode) : NULL; -} - -static int view_sam(hFILE *hfp, const char *filename) -{ - samFile *in = hts_hopen(hfp, filename, "r"); - bam_hdr_t *hdr = NULL; - samFile *out = NULL; - if (in == NULL) { - status = EXIT_FAILURE; - return 0; - } - hdr = sam_hdr_read(in); - if (hdr == NULL) { - status = EXIT_FAILURE; - goto clean; - } - out = dup_stdout("w"); - if (out == NULL) { - status = EXIT_FAILURE; - goto clean; - } - - if (show_headers) { - if (sam_hdr_write(out, hdr) != 0) { - status = EXIT_FAILURE; - goto clean; - } - } - if (mode == view_all) { - bam1_t *b = bam_init1(); - int ret; - while ((ret = sam_read1(in, hdr, b)) >= 0) { - if (sam_write1(out, hdr, b) < 0) { - status = EXIT_FAILURE; - goto clean; - } - } - bam_destroy1(b); - if (ret != -1) // eof - status = EXIT_FAILURE; - } - - clean: - if (hdr != NULL) bam_hdr_destroy(hdr); - if (out != NULL && hts_close(out) != 0) - status = EXIT_FAILURE; - if (hts_close(in) != 0) - status = EXIT_FAILURE; - return 1; -} - -static int view_vcf(hFILE *hfp, const char *filename) -{ - vcfFile *in = hts_hopen(hfp, filename, "r"); - bcf_hdr_t *hdr = NULL; - vcfFile *out = NULL; - if (in == NULL) { - status = EXIT_FAILURE; - return 0; - } - hdr = bcf_hdr_read(in); - if (hdr == NULL) { - status = EXIT_FAILURE; - goto clean; - } - out = dup_stdout("w"); - if (out == NULL) { - status = EXIT_FAILURE; - goto clean; - } - - if (show_headers) { - if (bcf_hdr_write(out, hdr) != 0) { - status = EXIT_FAILURE; - goto clean; - } - } - if (mode == view_all) { - bcf1_t *rec = bcf_init(); - while (bcf_read(in, hdr, rec) >= 0) { - if (bcf_write(out, hdr, rec) < 0) { - status = EXIT_FAILURE; - goto clean; - } - } - bcf_destroy(rec); - } - - clean: - if (hdr != NULL) bcf_hdr_destroy(hdr); - if (out != NULL) hts_close(out); - hts_close(in); - return 1; -} - -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++; break; - case 1: - printf( -"htsfile (htslib) %s\n" -"Copyright (C) 2015 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++) { - htsFormat fmt; - hFILE *fp = hopen(argv[i], "r"); - if (fp == NULL) { - fprintf(stderr, "htsfile: can't open \"%s\": %s\n", argv[i], strerror(errno)); - status = EXIT_FAILURE; - continue; - } - - if (hts_detect_format(fp, &fmt) < 0) { - fprintf(stderr, "htsfile: detecting \"%s\" format failed: %s\n", argv[i], strerror(errno)); - hclose_abruptly(fp); - status = EXIT_FAILURE; - continue; - } - - if (mode == identify) { - char *description = hts_format_description(&fmt); - printf("%s:\t%s\n", argv[i], description); - free(description); - } - else - switch (fmt.category) { - case sequence_data: - if (view_sam(fp, argv[i])) fp = NULL; - break; - case variant_data: - if (view_vcf(fp, argv[i])) fp = NULL; - break; - default: - fprintf(stderr, "htsfile: can't view %s: unknown format\n", argv[i]); - status = EXIT_FAILURE; - break; - } - - if (fp && hclose(fp) < 0) { - fprintf(stderr, "htsfile: closing %s failed\n", argv[i]); - status = EXIT_FAILURE; - } - } - - return status; -}