--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/hfile.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,204 @@
+/*  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;
+}