MonetDB: bamloader - Made sure the bam loader actually compiles....

[Robin Cijvat]

Changeset: 1cc79f6baa83 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=1cc79f6baa83
Modified Files:
        configure.ag
        sql/backends/monet5/bamloader/bam_loader.c
Branch: bamloader
Log Message:

Made sure the bam loader actually compiles. Next step: create stripped version 
of bam loader that only has core functionality.


diffs (81 lines):

diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2311,6 +2311,45 @@ AC_SUBST(MSEED_CFLAGS, $MSEED_CFLAGS)
 AC_SUBST(MSEED_LIBS, $MSEED_LIBS)
 AM_CONDITIONAL(HAVE_MSEED, test x"$have_mseed" != xno)
 
+# samtools, only used by sql
+have_samtools="auto"
+AC_ARG_WITH(samtools,
+    AS_HELP_STRING([--with-samtools=DIR],[samtools (providing bam library) are 
installed in DIR]),
+    [have_samtools="$withval"], [have_samtools="auto"])
+if test "x$have_samtools" != xno; then
+
+       case "$have_samtools" in
+       auto|yes)
+           ;;
+       *)
+           SAMTOOLS_CFLAGS="-I$have_samtools/include"
+           SAMTOOLS_LIBS="-L$have_samtools/lib -lbam"
+           ;;
+       esac
+
+       save_CPPFLAGS="$CPPFLAGS"
+       save_LDFLAGS="$LDFLAGS"
+       CPPFLAGS="$CPPFLAGS $SAMTOOLS_CFLAGS"
+       LDFLAGS="$LDFLAGS $SAMTOOLS_LIBS"
+       AC_CHECK_HEADER(bam.h,
+               AC_CHECK_HEADER(bgzf.h,
+                       AC_CHECK_LIB(bam, bam_header_read,
+                               AC_DEFINE(HAVE_SAMTOOLS, 1, [Define if you have 
the samtools (providing the bam library)]),
+                               [ if test "x$have_samtoouls" != xauto; then 
AC_MSG_ERROR([-lbam library not found]); fi; have_samtools=no ],
+                               [-lpthread -lz]),
+                       [ if test "x$have_samtools" != xauto; then 
AC_MSG_ERROR([bgzf.h header not found]); fi; have_samtools=no ]),
+               [ if test "x$have_samtools" != xauto; then AC_MSG_ERROR([bam.h 
header not found]); fi; have_samtools=no ])
+       LDFLAGS="$save_LDFLAGS"
+       CPPFLAGS="$save_CPPFLAGS"
+  if test "x$have_samtools" = "xyes" -o "x$have_samtools" = "xauto"; then
+           SAMTOOLS_CFLAGS=
+           SAMTOOLS_LIBS="-lbam"
+  fi
+fi
+AC_SUBST(SAMTOOLS_CFLAGS, $SAMTOOLS_CFLAGS)
+AC_SUBST(SAMTOOLS_LIBS, $SAMTOOLS_LIBS)
+AM_CONDITIONAL(HAVE_SAMTOOLS, test x"$have_samtools" != xno)
+
 # geos, only used in geom module
 org_have_geos=auto
 have_geos=$org_have_geos
diff --git a/sql/backends/monet5/bamloader/bam_loader.c 
b/sql/backends/monet5/bamloader/bam_loader.c
--- a/sql/backends/monet5/bamloader/bam_loader.c
+++ b/sql/backends/monet5/bamloader/bam_loader.c
@@ -1842,10 +1842,7 @@ bam_loader_repos(Client cntxt, MalBlkPtr
     }
     else
     {
-        _threads_data d = {
-            .max_nr_threads = nr_threads,
-            .thread_available = (bit *)GDKmalloc(nr_threads * sizeof(bit))
-        };
+        _threads_data d;
         pthread_t *threads = (pthread_t *)GDKzalloc(nr_threads * 
sizeof(pthread_t));
         _reader_thread_data *data = (_reader_thread_data 
*)GDKmalloc(nr_threads * sizeof(_reader_thread_data));
         
@@ -1855,6 +1852,7 @@ bam_loader_repos(Client cntxt, MalBlkPtr
         void **ret = GDKmalloc(MIN(nr_threads, nr_file_paths) * sizeof(str));
         
         int i;
+
         
         if(threads == NULL || d.thread_available == NULL || data == NULL || 
ret == NULL)
             throw(MAL, "bam_loader_repos", MAL_MALLOC_FAIL);
@@ -1862,6 +1860,8 @@ bam_loader_repos(Client cntxt, MalBlkPtr
         if(pthread_mutex_init(&current_file_lock, NULL) != 0 || 
pthread_mutex_init(&client_lock, NULL) != 0 || 
pthread_mutex_init(&d.threads_data_lock, NULL) != 0)
             throw(MAL, "bam_loader_repos", "Error on initializing mutex\n");
             
+        d.max_nr_threads = nr_threads;
+        d.thread_available = (bit *)GDKmalloc(nr_threads * sizeof(bit));
         for(i=0; i<nr_threads; ++i)
             d.thread_available[i] = TRUE;
             
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