7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/test/hfile.c src/htslib/test/hfile.c deleted file mode 100644 index c4ba91c4bca..00000000000 --- src/htslib/test/hfile.c +++ /dev/null @@ -1,204 +0,0 @@ -/* test/hfile.c -- Test cases for low-level input/output streams. - - Copyright (C) 2013-2014 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 <stdarg.h> -#include <stdio.h> -#include <stdlib.h> -#include <errno.h> - -#include <sys/stat.h> - -#include "htslib/hfile.h" -#include "htslib/hts_defs.h" - -void HTS_NORETURN fail(const char *format, ...) -{ - int err = errno; - va_list args; - va_start(args, format); - vfprintf(stderr, format, args); - va_end(args); - if (err != 0) fprintf(stderr, ": %s", strerror(err)); - fprintf(stderr, "\n"); - exit(EXIT_FAILURE); -} - -void check_offset(hFILE *f, off_t off, const char *message) -{ - off_t ret = htell(f); - if (ret < 0) fail("htell(%s)", message); - if (ret == off) return; - - fprintf(stderr, "%s offset incorrect: expected %ld but got %ld\n", - message, (long)off, (long)ret); - exit(EXIT_FAILURE); -} - -char *slurp(const char *filename) -{ - char *text; - struct stat sbuf; - size_t filesize; - FILE *f = fopen(filename, "r"); - if (f == NULL) fail("fopen(\"%s\", \"r\")", filename); - if (fstat(fileno(f), &sbuf) != 0) fail("fstat(\"%s\")", filename); - filesize = sbuf.st_size; - - text = (char *) malloc(filesize + 1); - if (text == NULL) fail("malloc(text)"); - - if (fread(text, 1, filesize, f) != filesize) fail("fread"); - fclose(f); - - text[filesize] = '\0'; - return text; -} - -hFILE *fin = NULL; -hFILE *fout = NULL; - -void reopen(const char *infname, const char *outfname) -{ - if (fin) { if (hclose(fin) != 0) fail("hclose(input)"); } - if (fout) { if (hclose(fout) != 0) fail("hclose(output)"); } - - fin = hopen(infname, "r"); - if (fin == NULL) fail("hopen(\"%s\")", infname); - - fout = hopen(outfname, "w"); - if (fout == NULL) fail("hopen(\"%s\")", outfname); -} - -int main(void) -{ - static const int size[] = { 1, 13, 403, 999, 30000 }; - - char buffer[40000]; - char *original; - int c, i; - ssize_t n; - off_t off; - - reopen("vcf.c", "test/hfile1.tmp"); - while ((c = hgetc(fin)) != EOF) { - if (hputc(c, fout) == EOF) fail("hputc"); - } - if (herrno(fin)) { errno = herrno(fin); fail("hgetc"); } - - reopen("test/hfile1.tmp", "test/hfile2.tmp"); - if (hpeek(fin, buffer, 50) < 0) fail("hpeek"); - while ((n = hread(fin, buffer, 17)) > 0) { - if (hwrite(fout, buffer, n) != n) fail("hwrite"); - } - if (n < 0) fail("hread"); - - reopen("test/hfile2.tmp", "test/hfile3.tmp"); - while ((n = hread(fin, buffer, sizeof buffer)) > 0) { - if (hwrite(fout, buffer, n) != n) fail("hwrite"); - if (hpeek(fin, buffer, 700) < 0) fail("hpeek"); - } - if (n < 0) fail("hread"); - - reopen("test/hfile3.tmp", "test/hfile4.tmp"); - i = 0; - off = 0; - while ((n = hread(fin, buffer, size[i++ % 5])) > 0) { - off += n; - buffer[n] = '\0'; - check_offset(fin, off, "pre-peek"); - if (hputs(buffer, fout) == EOF) fail("hputs"); - if ((n = hpeek(fin, buffer, size[(i+3) % 5])) < 0) fail("hpeek"); - check_offset(fin, off, "post-peek"); - } - if (n < 0) fail("hread"); - - reopen("test/hfile4.tmp", "test/hfile5.tmp"); - n = hread(fin, buffer, 200); - if (n < 0) fail("hread"); - else if (n != 200) fail("hread only got %d", (int)n); - if (hwrite(fout, buffer, 1000) != 1000) fail("hwrite"); - check_offset(fin, 200, "input/first200"); - check_offset(fout, 1000, "output/first200"); - - if (hseek(fin, 800, SEEK_CUR) < 0) fail("hseek/cur"); - check_offset(fin, 1000, "input/seek"); - for (off = 1000; (n = hread(fin, buffer, sizeof buffer)) > 0; off += n) - if (hwrite(fout, buffer, n) != n) fail("hwrite"); - if (n < 0) fail("hread"); - check_offset(fin, off, "input/eof"); - check_offset(fout, off, "output/eof"); - - if (hseek(fin, 200, SEEK_SET) < 0) fail("hseek/set"); - if (hseek(fout, 200, SEEK_SET) < 0) fail("hseek(output)"); - check_offset(fin, 200, "input/backto200"); - check_offset(fout, 200, "output/backto200"); - n = hread(fin, buffer, 800); - if (n < 0) fail("hread"); - else if (n != 800) fail("hread only got %d", (int)n); - if (hwrite(fout, buffer, 800) != 800) fail("hwrite"); - check_offset(fin, 1000, "input/wrote800"); - check_offset(fout, 1000, "output/wrote800"); - - if (hflush(fout) == EOF) fail("hflush"); - - original = slurp("vcf.c"); - for (i = 1; i <= 5; i++) { - char *text; - sprintf(buffer, "test/hfile%d.tmp", i); - text = slurp(buffer); - if (strcmp(original, text) != 0) { - fprintf(stderr, "%s differs from vcf.c\n", buffer); - return EXIT_FAILURE; - } - free(text); - } - free(original); - - if (hclose(fin) != 0) fail("hclose(input)"); - if (hclose(fout) != 0) fail("hclose(output)"); - - fout = hopen("test/hfile_chars.tmp", "w"); - if (fout == NULL) fail("hopen(\"test/hfile_chars.tmp\")"); - for (i = 0; i < 256; i++) - if (hputc(i, fout) != i) fail("chars: hputc (%d)", i); - if (hclose(fout) != 0) fail("hclose(test/hfile_chars.tmp)"); - - fin = hopen("test/hfile_chars.tmp", "r"); - if (fin == NULL) fail("hopen(\"test/hfile_chars.tmp\") for reading"); - for (i = 0; i < 256; i++) - if ((c = hgetc(fin)) != i) - fail("chars: hgetc (%d = 0x%x) returned %d = 0x%x", i, i, c, c); - if ((c = hgetc(fin)) != EOF) fail("chars: hgetc (EOF) returned %d", c); - if (hclose(fin) != 0) fail("hclose(test/hfile_chars.tmp) for reading"); - - fin = hopen("data:hello, world!\n", "r"); - if (fin == NULL) fail("hopen(\"data:...\")"); - n = hread(fin, buffer, 300); - if (n < 0) fail("hread"); - buffer[n] = '\0'; - if (strcmp(buffer, "hello, world!\n") != 0) fail("hread result"); - if (hclose(fin) != 0) fail("hclose(\"data:...\")"); - - return EXIT_SUCCESS; -}