Changeset: 75d290290e13 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=75d290290e13
Added Files:
sql/backends/monet5/bamloader/mykstring.h
Modified Files:
configure.ag
sql/backends/monet5/bamloader/bam_wrapper.c
Branch: bamloader
Log Message:
Include private version of kstring.h for Ubuntu.
diffs (160 lines):
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2425,6 +2425,7 @@ if test "x$have_samtools" != xno; then
if test "x$have_samtools" = "xyes" -o "x$have_samtools" = "xauto"; then
SAMTOOLS_CFLAGS=
SAMTOOLS_LIBS="-lbam"
+ AC_CHECK_HEADERS([samtools/kstring.h])
fi
fi
AC_SUBST(SAMTOOLS_CFLAGS, $SAMTOOLS_CFLAGS)
diff --git a/sql/backends/monet5/bamloader/bam_wrapper.c
b/sql/backends/monet5/bamloader/bam_wrapper.c
--- a/sql/backends/monet5/bamloader/bam_wrapper.c
+++ b/sql/backends/monet5/bamloader/bam_wrapper.c
@@ -26,11 +26,16 @@
#include "stream.h"
#include <samtools/bam.h>
+#ifdef HAVE_SAMTOOLS_KSTRING_H
#include <samtools/kstring.h>
+#else
+/* Ubuntu doesn't distribute samtools/kstring.h, so we need our own
+ * version */
+#include "mykstring.h"
+#endif
#include "bam_globals.h"
#include "bam_wrapper.h"
-
str
ordering_str(ordering ord)
{
diff --git a/sql/backends/monet5/bamloader/mykstring.h
b/sql/backends/monet5/bamloader/mykstring.h
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bamloader/mykstring.h
@@ -0,0 +1,123 @@
+/* This is an extract from kstring.h from the samtools sources. It is
+ * included because the libbam-dev package on Ubuntu doesn't include
+ * kstring.h. The copyright message is the one from samtools. */
+
+/* The MIT License
+
+ Copyright (c) by Attractive Chaos <[email protected]>
+
+ 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.
+*/
+
+#ifndef KSTRING_T
+typedef struct {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4,
(x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+
+static int ksprintf(kstring_t *s, const char *fmt, ...)
+ __attribute__((__format__(__printf__, 2, 3)));
+static int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+ va_list ap;
+ int l;
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not
work with glibc 2.0. See `man snprintf'.
+ va_end(ap);
+ if ((size_t) l + 1 > s->m - s->l) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+ }
+ va_end(ap);
+ s->l += l;
+ return l;
+}
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
+{
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ memcpy(s->s + s->l, p, l);
+ s->l += l;
+ s->s[s->l] = 0;
+ return l;
+}
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+ return kputsn(p, strlen(p), s);
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+ if (s->l + 1 >= s->m) {
+ s->m = s->l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ s->s[s->l++] = c;
+ s->s[s->l] = 0;
+ return c;
+}
+
+static inline int kputw(int c, kstring_t *s)
+{
+ char buf[16];
+ int l, x;
+ if (c == 0) return kputc('0', s);
+ if(c < 0) for (l = 0, x = c; x < 0; x /= 10) buf[l++] = '0' - (x%10);
+ else for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (c < 0) buf[l++] = '-';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+ s->s[s->l] = 0;
+ return 0;
+}
+
+static inline int kputuw(unsigned c, kstring_t *s)
+{
+ char buf[16];
+ int l, i;
+ unsigned x;
+ if (c == 0) return kputc('0', s);
+ for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+ s->s[s->l] = 0;
+ return 0;
+}
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