11e45667d4e291b3038ccda729a1cdf5bcaf004a braney Mon Jul 11 15:46:54 2016 -0700 incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX defines, modify a bunch of makefiles to include kentSrc variable pointing to top of the tree. diff --git src/htslib/htsfile.c src/htslib/htsfile.c new file mode 100644 index 0000000..bfd0a74 --- /dev/null +++ src/htslib/htsfile.c @@ -0,0 +1,234 @@ +/* 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; +}