Changeset: ba1a7909e081 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ba1a7909e081
Modified Files:
sql/backends/monet5/bam/Tests/common/common.c
sql/backends/monet5/bam/Tests/common/common.h
sql/backends/monet5/bam/Tests/db_exec/db_exec
sql/backends/monet5/bam/Tests/db_exec/db_exec.c
sql/backends/monet5/bam/Tests/usecase_exec/data_table.c
sql/backends/monet5/bam/Tests/usecase_exec/usecase_exec
sql/backends/monet5/bam/Tests/usecase_exec/usecase_exec.c
sql/backends/monet5/bam/bam_loader.c
sql/backends/monet5/bam/bam_loader.h
Branch: DVframework_bam
Log Message:
Fixed last memory leaks in db_exec and usecase_exec and fixed as many as
possible in bam_loader. Furthermore, prepared the three programs for the test
runs on bricks10
diffs (truncated from 4884 to 300 lines):
diff --git a/sql/backends/monet5/bam/Tests/common/common.c
b/sql/backends/monet5/bam/Tests/common/common.c
--- a/sql/backends/monet5/bam/Tests/common/common.c
+++ b/sql/backends/monet5/bam/Tests/common/common.c
@@ -3,8 +3,71 @@
#include <sys/stat.h>
#include "common.h"
-str bam_filenames[NR_BAMFILES] = {"venter-chr22-100k.stampy.bam",
"venter-chr22-100k.bwa.bam"};
-int bam_filename_pairs[NR_BAMFILE_PAIRS][2] = {{0, 1}};
+/* Local test setting */
+str bam_filenames[NR_BAMFILES] = {
+ "venter-chr22-100k.stampy.bam",
+ "venter-chr22-100k.bwa.bam"
+};
+int bam_filename_pairs[NR_BAMFILE_PAIRS][2] = {
+ {0, 1}
+};
+
+
+/* All small BAM files
+str bam_filenames[NR_BAMFILES] = {
+ "venter-chr22-100k.stampy.bam",
+ "venter-chr22-100k.misterl-bwa.bam",
+ "venter-chr22-100k.bowtie.bam",
+ "venter-chr22-100k.bwa.bam",
+ "venter-chr22-100k.split.bwa.bam",
+ "venter-1000th.misterl-bwa.bam",
+ "venter-1000th.split.bwa.bam",
+ "venter-chr22.stampy.bam",
+ "venter-chr22.bowtie.bam",
+ "venter-chr22.bowtie-local.bam",
+ "venter-chr22.bwa.bam",
+ "venter-chr22.bowtie-multi.bam",
+ "venter-chr22.misterl-bwa-snps.bam",
+ "venter-chr22.misterl-bwa.bam",
+ "venter-chr22.split.bwa.bam"
+};
+
+int bam_filename_pairs[NR_BAMFILE_PAIRS][2] = {
+ {0 , 1 },
+ {1 , 2 },
+ {2 , 3 },
+ {3 , 4 },
+ {4 , 5 },
+ {5 , 6 },
+ {6 , 7 },
+ {7 , 8 },
+ {8 , 9 },
+ {9 , 10},
+ {10, 11},
+ {11, 12},
+ {12, 13},
+ {13, 14},
+ {0 , 14}
+};
+*/
+
+/* All big BAM files
+str bam_filenames[NR_BAMFILES] = {
+ "venter.stampy.bam",
+ "venter.bowtie.bam",
+ "venter.bwa.bam",
+ "venter.bowtie-multi.bam",
+ "venter.split.bowtie.bam"
+};
+
+int bam_filename_pairs[NR_BAMFILE_PAIRS][2] = {
+ {0, 1},
+ {1, 2},
+ {2, 3},
+ {3, 4},
+ {0, 4}
+};
+*/
str sortingcols1[] = {
"1",
diff --git a/sql/backends/monet5/bam/Tests/common/common.h
b/sql/backends/monet5/bam/Tests/common/common.h
--- a/sql/backends/monet5/bam/Tests/common/common.h
+++ b/sql/backends/monet5/bam/Tests/common/common.h
@@ -11,10 +11,11 @@
#define DB_A 0 /* Always either (UNSORTED, QUERYNAME and COORDINATE) or
(DB_A or DB_B) will be used by either usecase_exec or db_exec respectively */
#define DB_B 1
-#define BAM_REPOS "/export/scratch2/robin/bam"
-#define DIR_OUTPUT "/export/scratch2/robin/output"
-#define DIR_STATS_OUTPUT "/export/scratch2/robin/output"
-#define DIR_USECASES
"/export/scratch2/robin/Monet/SOURCE/MonetDB/sql/backends/monet5/bam/Tests"
+#define HOME "/export/scratch2/robin"
+#define BAM_REPOS HOME"/bam"
+#define DIR_OUTPUT HOME"/output"
+#define DIR_STATS_OUTPUT HOME"/output"
+#define DIR_USECASES HOME"/Monet/SOURCE/MonetDB/sql/backends/monet5/bam/Tests"
#define DIR_BENCHMARKS_0 "benchmarks_0"
#define DIR_BENCHMARKS_1 "benchmarks_1"
@@ -43,9 +44,21 @@
#define min( a, b ) ( ((a) < (b)) ? (a) : (b) )
#define max( a, b ) ( ((a) > (b)) ? (a) : (b) )
+/* Local test setting */
#define NR_BAMFILES 2
#define NR_BAMFILE_PAIRS 1
+
+/* Small BAM files
+#define NR_BAM_FILES 15
+#define NR_BAMFILE_PAIRS 15
+*/
+
+/* Big BAM files
+#define NR_BAM_FILES 5
+#define NR_BAMFILE_PAIRS 5
+*/
+
extern str bam_filenames[NR_BAMFILES];
extern int bam_filename_pairs[NR_BAMFILE_PAIRS][2];
diff --git a/sql/backends/monet5/bam/Tests/db_exec/db_exec
b/sql/backends/monet5/bam/Tests/db_exec/db_exec
index
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