Changeset: 1cd2e21d1783 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=1cd2e21d1783
Modified Files:
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.10a.sql
sql/backends/monet5/bam/Tests/benchmarks_0/query2.1a.sql
sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
sql/backends/monet5/bam/Tests/common/common.h
sql/backends/monet5/bam/Tests/common/stats.c
sql/backends/monet5/bam/Tests/db_exec/db_exec
sql/backends/monet5/bam/Tests/db_exec/db_exec.c
sql/backends/monet5/bam/Tests/db_exec/makefile
sql/backends/monet5/bam/Tests/usecase_exec/usecase_exec
sql/backends/monet5/bam/bam_loader.c
sql/backends/monet5/bam/bam_sql.c
sql/backends/monet5/bam/bam_sql.h
Branch: DVframework_bam
Log Message:
Fixed some errors in the benchmark queries and some other small things.
diffs (truncated from 4923 to 300 lines):
diff --git a/sql/backends/monet5/bam/Makefile.ag
b/sql/backends/monet5/bam/Makefile.ag
--- a/sql/backends/monet5/bam/Makefile.ag
+++ b/sql/backends/monet5/bam/Makefile.ag
@@ -34,7 +34,7 @@ INCLUDES = .. \
lib__bam = {
MODULE
DIR = libdir/monetdb5
- SOURCES = bam_loader.c bam_loader.h bam_lib.h bam_lib.c
+ SOURCES = bam_loader.c bam_loader.h bam_lib.h bam_lib.c bam_sql.h
bam_sql.c
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
../../../../gdk/libbat \
$(SAMTOOLS_LIBS)
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
b/sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_0/benchmark2.sql
@@ -5,7 +5,7 @@
WITH qnames AS (
SELECT qname
FROM bam.alignments_i
- AND seq <> '*'
+ WHERE seq <> '*'
AND qual <> '*'
AND bam_flag(flag, 'firs_segm') <> bam_flag(flag, 'last_segm')
AND bam_flag(flag, 'seco_alig') = False
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_0/query2.10a.sql
b/sql/backends/monet5/bam/Tests/benchmarks_0/query2.10a.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_0/query2.10a.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_0/query2.10a.sql
@@ -19,7 +19,7 @@ FROM (
AND rname = rname_2_10
AND bam_flag(flag, 'seco_alig') = False
AND bam_flag(flag, 'firs_segm') = True
- AND qnames IN (
+ AND qname IN (
SELECT *
FROM qnames
)
@@ -30,7 +30,7 @@ FROM (
AND rname = rname_2_10
AND bam_flag(flag, 'seco_alig') = False
AND bam_flag(flag, 'last_segm') = True
- AND qnames IN (
+ AND qname IN (
SELECT *
FROM qnames
)
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_0/query2.1a.sql
b/sql/backends/monet5/bam/Tests/benchmarks_0/query2.1a.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_0/query2.1a.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_0/query2.1a.sql
@@ -1,7 +1,7 @@
WITH qnames AS (
SELECT qname
FROM bam.alignments_i
- AND seq <> '*'
+ WHERE seq <> '*'
AND qual <> '*'
AND bam_flag(flag, 'firs_segm') <> bam_flag(flag, 'last_segm')
AND bam_flag(flag, 'seco_alig') = False
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/benchmark2.sql
@@ -9,9 +9,12 @@ SELECT qname,
CASE WHEN bam_flag(r_flag, 'segm_reve') THEN reverse_seq(r_seq) ELSE
r_seq END AS r_seq,
CASE WHEN bam_flag(r_flag, 'segm_reve') THEN reverse_qual(r_qual) ELSE
r_qual END AS r_qual
FROM bam.paired_primary_alignments_i
-WHERE seq <> '*'
- AND qual <> '*'
- AND mapq < mapq_2_1
+WHERE l_seq <> '*'
+ AND l_qual <> '*'
+ AND l_mapq < mapq_2_1
+ AND r_seq <> '*'
+ AND r_qual <> '*'
+ AND r_mapq < mapq_2_1
ORDER BY qname;
@@ -34,7 +37,7 @@ SELECT
ELSE l_pos - (r_pos + seq_length(r_cigar))
END AS distance,
COUNT(*) AS nr_alignments
-FROM paired_primary_alignments_i
+FROM bam.paired_primary_alignments_i
WHERE l_rname = r_rname
GROUP BY distance
ORDER BY nr_alignments DESC;
@@ -57,7 +60,7 @@ SELECT qname, flag, rname, pos, mapq, ci
FROM bam.unpaired_all_alignments_i
WHERE qname IN (
SELECT qname
- FROM bam.unpaired_all_alignments
+ FROM bam.unpaired_all_alignments_i
GROUP BY qname
HAVING SUM(bam_flag(flag, 'firs_segm')) = 0
OR SUM(bam_flag(flag, 'last_segm')) = 0
@@ -230,7 +233,7 @@ FROM (
SELECT *
FROM bam.unpaired_primary_alignments_j
) AS f2
- ON l.qname = r.qname
+ ON f1.qname = f2.qname
AND bam_flag(f1.flag, 'firs_segm') = bam_flag(f2.flag, 'firs_segm')
AND (f1.rname <> f2.rname OR f1.pos <> f2.pos)
ORDER BY qname;
@@ -275,8 +278,8 @@ FROM bam.paired_primary_alignments_i
WHERE l_rname = rname_2_10
AND r_rname = rname_2_10
AND CASE WHEN l_pos < r_pos
- THEN (pos_2_10 >= l.pos + seq_length(l.cigar) AND pos_2_10 < r.pos)
- ELSE (pos_2_10 >= r.pos + seq_length(r.cigar) AND pos_2_10 < l.pos)
+ THEN (pos_2_10 >= l_pos + seq_length(l_cigar) AND pos_2_10 < r_pos)
+ ELSE (pos_2_10 >= r_pos + seq_length(r_cigar) AND pos_2_10 < l_pos)
END
ORDER BY l_pos
@@ -317,7 +320,7 @@ ORDER BY qname;
WITH alig AS (
SELECT *
- FROM unpaired_alignments_i
+ FROM bam.unpaired_alignments_i
WHERE bam_flag(flag, 'firs_segm') <> bam_flag(flag, 'last_segm')
AND bam_flag(flag, 'seco_alig') = True
AND rnext = '*'
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.1.sql
@@ -4,7 +4,10 @@ SELECT qname,
CASE WHEN bam_flag(r_flag, 'segm_reve') THEN reverse_seq(r_seq) ELSE
r_seq END AS r_seq,
CASE WHEN bam_flag(r_flag, 'segm_reve') THEN reverse_qual(r_qual) ELSE
r_qual END AS r_qual
FROM bam.paired_primary_alignments_i
-WHERE seq <> '*'
- AND qual <> '*'
- AND mapq < mapq_2_1
+WHERE l_seq <> '*'
+ AND l_qual <> '*'
+ AND l_mapq < mapq_2_1
+ AND r_seq <> '*'
+ AND r_qual <> '*'
+ AND r_mapq < mapq_2_1
ORDER BY qname;
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.10.sql
@@ -4,7 +4,7 @@ FROM bam.paired_primary_alignments_i
WHERE l_rname = rname_2_10
AND r_rname = rname_2_10
AND CASE WHEN l_pos < r_pos
- THEN (pos_2_10 >= l.pos + seq_length(l.cigar) AND pos_2_10 < r.pos)
- ELSE (pos_2_10 >= r.pos + seq_length(r.cigar) AND pos_2_10 < l.pos)
+ THEN (pos_2_10 >= l_pos + seq_length(l_cigar) AND pos_2_10 < r_pos)
+ ELSE (pos_2_10 >= r_pos + seq_length(r_cigar) AND pos_2_10 < l_pos)
END
ORDER BY l_pos
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.12.sql
@@ -1,6 +1,6 @@
WITH alig AS (
SELECT *
- FROM unpaired_alignments_i
+ FROM bam.unpaired_alignments_i
WHERE bam_flag(flag, 'firs_segm') <> bam_flag(flag, 'last_segm')
AND bam_flag(flag, 'seco_alig') = True
AND rnext = '*'
@@ -30,4 +30,4 @@ FROM (
) AS alig
WHERE distance > 0
AND distance < distance_2_12
-ORDER BY rname;
+ORDER BY rname;
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.2.sql
@@ -4,7 +4,7 @@ SELECT
ELSE l_pos - (r_pos + seq_length(r_cigar))
END AS distance,
COUNT(*) AS nr_alignments
-FROM paired_primary_alignments_i
+FROM bam.paired_primary_alignments_i
WHERE l_rname = r_rname
GROUP BY distance
ORDER BY nr_alignments DESC;
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.3.sql
@@ -2,7 +2,7 @@ SELECT qname, flag, rname, pos, mapq, ci
FROM bam.unpaired_all_alignments_i
WHERE qname IN (
SELECT qname
- FROM bam.unpaired_all_alignments
+ FROM bam.unpaired_all_alignments_i
GROUP BY qname
HAVING SUM(bam_flag(flag, 'firs_segm')) = 0
OR SUM(bam_flag(flag, 'last_segm')) = 0
diff --git a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
--- a/sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
+++ b/sql/backends/monet5/bam/Tests/benchmarks_1/query2.8.sql
@@ -9,7 +9,7 @@ FROM (
SELECT *
FROM bam.unpaired_primary_alignments_j
) AS f2
- ON l.qname = r.qname
+ ON f1.qname = f2.qname
AND bam_flag(f1.flag, 'firs_segm') = bam_flag(f2.flag, 'firs_segm')
AND (f1.rname <> f2.rname OR f1.pos <> f2.pos)
ORDER BY qname;
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
@@ -8,7 +8,8 @@
#define UNSORTED 0
#define QUERYNAME 1
#define COORDINATE 2
-#define DB 0 /* Always either UNSORTED, QUERYNAME and COORDINATE or DB
will be used by either usecase_exec or db_exec respectively */
+#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"
diff --git a/sql/backends/monet5/bam/Tests/common/stats.c
b/sql/backends/monet5/bam/Tests/common/stats.c
--- a/sql/backends/monet5/bam/Tests/common/stats.c
+++ b/sql/backends/monet5/bam/Tests/common/stats.c
@@ -17,21 +17,24 @@ void init_usecase_timestats(usecase_time
void initialize_timestats(timestats *stats, bit benchmark1, bit benchmark2,
bit usecase_exec)
{
int i, j;
- int nr_methods;
+ int nr_methods_init, nr_methods_bm1, nr_methods_bm2;
stats->benchmark1 = benchmark1;
stats->benchmark2 = benchmark2;
stats->usecase_exec = usecase_exec;
- nr_methods = usecase_exec ? 3 : 1;
- for(i=0; i<nr_methods; ++i)
+ nr_methods_init = usecase_exec ? 3 : 1; /* In this case, only DB_A will be
used */
+ nr_methods_bm1 = usecase_exec ? 3 : 1; /* In this case, only DB_A will be
used */
+ nr_methods_bm2 = usecase_exec ? 3 : 2;
+
+ for(i=0; i<nr_methods_init; ++i)
{
stats->init_stats[i].init_times_sec = (double *)calloc(NR_BAMFILES,
sizeof(double));
}
if(benchmark1)
{
- for(i=0; i<nr_methods; ++i)
+ for(i=0; i<nr_methods_bm1; ++i)
{
stats->usecase_stats_bm1[i] = (usecase_timestats *)malloc(5 *
sizeof(usecase_timestats));
for(j=0; j<5; ++j)
@@ -42,7 +45,7 @@ void initialize_timestats(timestats *sta
}
if(benchmark2)
{
- for(i=0; i<nr_methods; ++i)
+ for(i=0; i<nr_methods_bm2; ++i)
{
stats->usecase_stats_bm2[i] = (usecase_timestats *)malloc(12 *
sizeof(usecase_timestats));
for(j=0; j<4; ++j)
@@ -63,17 +66,19 @@ void initialize_timestats(timestats *sta
void clear_timestats(timestats *stats)
{
+ int nr_methods_init = stats->usecase_exec ? 3 : 1; /* In this case, only
DB_A will be used */
+ int nr_methods_bm1 = stats->usecase_exec ? 3 : 1; /* In this case, only
DB_A will be used */
+ int nr_methods_bm2 = stats->usecase_exec ? 3 : 2;
int i, j;
- int nr_methods = stats->usecase_exec ? 3 : 1;
- for(i=0; i<nr_methods; ++i)
+ for(i=0; i<nr_methods_init; ++i)
{
free(stats->init_stats[i].init_times_sec);
}
if(stats->benchmark1)
{
- for(i=0; i<nr_methods; ++i)
+ for(i=0; i<nr_methods_bm1; ++i)
{
for(j=0; j<5; ++j)
{
@@ -91,7 +96,7 @@ void clear_timestats(timestats *stats)
}
if(stats->benchmark2)
{
- for(i=0; i<nr_methods; ++i)
+ for(i=0; i<nr_methods_bm2; ++i)
{
for(j=0; j<12; ++j)
{
@@ -142,7 +147,8 @@ void write_init_timestats(FILE *output,
}
else
{
- write_times_sec(output, "bam_loader_file", stats[DB].init_times_sec,
NR_BAMFILES);
+ write_times_sec(output, "bam_loader_file", stats[DB_A].init_times_sec,
NR_BAMFILES);
+ write_times_sec(output, "bam_loader_file", stats[DB_B].init_times_sec,
NR_BAMFILES);
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