Changeset: 2f317aade056 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=2f317aade056
Modified Files:
clients/mapiclient/mclient.c
configure.ag
sql/backends/monet5/bamloader/85_bam.mal
sql/backends/monet5/bamloader/Makefile.ag
sql/backends/monet5/bamloader/Tests/All
sql/backends/monet5/bamloader/Tests/benchmarks.py
sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.1.sql
sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.8.sql
sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.1.sql
sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.12.sql
sql/backends/monet5/bamloader/Tests/load.sql.src
sql/backends/monet5/bamloader/Tests/sort.cmd.src
Branch: bamloader
Log Message:
Layout.
Use consistent layout in mclient.c; files should end with a newline.
diffs (truncated from 329 to 300 lines):
diff --git a/clients/mapiclient/mclient.c b/clients/mapiclient/mclient.c
--- a/clients/mapiclient/mclient.c
+++ b/clients/mapiclient/mclient.c
@@ -75,12 +75,6 @@
#endif
#endif
-/* Samtools is not needed for the SAMrenderer, so commented out
-#ifdef HAVE_SAMTOOLS
-#include "bam.h"
-#endif
-*/
-
#ifndef S_ISCHR
#define S_ISCHR(m) (((m) & S_IFMT) == S_IFCHR)
#endif
@@ -123,7 +117,7 @@ enum formatters {
TESTformatter,
CLEANformatter,
TIMERformatter,
- SAMformatter
+ SAMformatter
};
static enum formatters formatter = NOformatter;
char *output = NULL; /* output format as string */
@@ -1041,75 +1035,80 @@ TIMERrenderer(MapiHdl hdl)
static void
SAMrenderer(MapiHdl hdl)
{
- /* Variables keeping track of which result set fields map to qname, flag
etc. (-1 means that it does not occur in result set) */
- int field_qname = -1;
- int field_flag = -1;
- int field_rname = -1;
- int field_pos = -1;
- int field_mapq = -1;
- int field_cigar = -1;
- int field_rnext = -1;
- int field_pnext = -1;
- int field_tlen = -1;
- int field_seq = -1;
- int field_qual = -1;
-
- int field_count = mapi_get_field_count(hdl);
- int t_fields;
-
- int i;
+ /* Variables keeping track of which result set fields map to
+ * qname, flag etc. (-1 means that it does not occur in result
+ * set) */
+ int field_qname = -1;
+ int field_flag = -1;
+ int field_rname = -1;
+ int field_pos = -1;
+ int field_mapq = -1;
+ int field_cigar = -1;
+ int field_rnext = -1;
+ int field_pnext = -1;
+ int field_tlen = -1;
+ int field_seq = -1;
+ int field_qual = -1;
-/* Samtools is not needed for rendering to SAM, so this is commented out
-#ifndef HAVE_SAMTOOLS
- mnstr_printf(toConsole, "Result set can not be rendered to BAM file, since
Samtools could not be found during compilation of mclient\n");
- return;
-#endif
-*/
+ int field_count = mapi_get_field_count(hdl);
+ int t_fields;
- /* First, initialize field variables properly */
- for(i=0; i<field_count; ++i) {
- char *field_name = mapi_get_name(hdl, i);
- if(strcmp(field_name, "qname") == 0) { field_qname = i; continue; }
- if(strcmp(field_name, "flag" ) == 0) { field_flag = i; continue; }
- if(strcmp(field_name, "rname") == 0) { field_rname = i; continue; }
- if(strcmp(field_name, "pos" ) == 0) { field_pos = i; continue; }
- if(strcmp(field_name, "mapq" ) == 0) { field_mapq = i; continue; }
- if(strcmp(field_name, "cigar") == 0) { field_cigar = i; continue; }
- if(strcmp(field_name, "rnext") == 0) { field_rnext = i; continue; }
- if(strcmp(field_name, "pnext") == 0) { field_pnext = i; continue; }
- if(strcmp(field_name, "tlen" ) == 0) { field_tlen = i; continue; }
- if(strcmp(field_name, "seq" ) == 0) { field_seq = i; continue; }
- if(strcmp(field_name, "qual" ) == 0) { field_qual = i; continue; }
-
- mnstr_printf(stderr_stream, "Unexpected column name in result set:
'%s'. Data in this column is not used.\n", field_name);
- }
-
- /* Write all alignments */
- while (!mnstr_errnr(toConsole) && (t_fields = fetch_row(hdl)) != 0) {
- if (t_fields != field_count) {
+ int i;
+
+ /* First, initialize field variables properly */
+ for (i = 0; i < field_count; i++) {
+ char *field_name = mapi_get_name(hdl, i);
+ if (strcmp(field_name, "qname") == 0)
+ field_qname = i;
+ else if (strcmp(field_name, "flag" ) == 0)
+ field_flag = i;
+ else if (strcmp(field_name, "rname") == 0)
+ field_rname = i;
+ else if (strcmp(field_name, "pos" ) == 0)
+ field_pos = i;
+ else if (strcmp(field_name, "mapq" ) == 0)
+ field_mapq = i;
+ else if (strcmp(field_name, "cigar") == 0)
+ field_cigar = i;
+ else if (strcmp(field_name, "rnext") == 0)
+ field_rnext = i;
+ else if (strcmp(field_name, "pnext") == 0)
+ field_pnext = i;
+ else if (strcmp(field_name, "tlen" ) == 0)
+ field_tlen = i;
+ else if (strcmp(field_name, "seq" ) == 0)
+ field_seq = i;
+ else if (strcmp(field_name, "qual" ) == 0)
+ field_qual = i;
+ else
+ mnstr_printf(stderr_stream, "Unexpected column name in
result set: '%s'. Data in this column is not used.\n", field_name);
+ }
+
+ /* Write all alignments */
+ while (!mnstr_errnr(toConsole) && (t_fields = fetch_row(hdl)) != 0) {
+ if (t_fields != field_count) {
mnstr_printf(stderr_stream,
- "invalid tuple received from server, "
- "got %d columns, expected %d,
ignoring\n", t_fields, field_count);
+ "invalid tuple received from server, "
+ "got %d columns, expected %d, ignoring\n",
t_fields, field_count);
continue;
- }
-
- /* Write fields to SAM line */
- mnstr_printf(toConsole, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
- (field_qname == -1 ? "*" : mapi_fetch_field(hdl, field_qname)),
- (field_flag == -1 ? "0" : mapi_fetch_field(hdl, field_flag )),
- (field_rname == -1 ? "*" : mapi_fetch_field(hdl, field_rname)),
- (field_pos == -1 ? "0" : mapi_fetch_field(hdl, field_pos )),
- (field_mapq == -1 ? "255" : mapi_fetch_field(hdl, field_mapq )),
- (field_cigar == -1 ? "*" : mapi_fetch_field(hdl, field_cigar)),
- (field_rnext == -1 ? "*" : mapi_fetch_field(hdl, field_rnext)),
- (field_pnext == -1 ? "0" : mapi_fetch_field(hdl, field_pnext)),
- (field_tlen == -1 ? "0" : mapi_fetch_field(hdl, field_tlen )),
- (field_seq == -1 ? "*" : mapi_fetch_field(hdl, field_seq )),
- (field_qual == -1 ? "*" : mapi_fetch_field(hdl, field_qual)));
- }
+ }
+
+ /* Write fields to SAM line */
+ mnstr_printf(toConsole,
"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
+ (field_qname == -1 ? "*" : mapi_fetch_field(hdl,
field_qname)),
+ (field_flag == -1 ? "0" : mapi_fetch_field(hdl,
field_flag )),
+ (field_rname == -1 ? "*" : mapi_fetch_field(hdl,
field_rname)),
+ (field_pos == -1 ? "0" : mapi_fetch_field(hdl,
field_pos )),
+ (field_mapq == -1 ? "255" : mapi_fetch_field(hdl,
field_mapq )),
+ (field_cigar == -1 ? "*" : mapi_fetch_field(hdl,
field_cigar)),
+ (field_rnext == -1 ? "*" : mapi_fetch_field(hdl,
field_rnext)),
+ (field_pnext == -1 ? "0" : mapi_fetch_field(hdl,
field_pnext)),
+ (field_tlen == -1 ? "0" : mapi_fetch_field(hdl,
field_tlen )),
+ (field_seq == -1 ? "*" : mapi_fetch_field(hdl,
field_seq )),
+ (field_qual == -1 ? "*" : mapi_fetch_field(hdl,
field_qual)));
+ }
}
-
static void
SQLheader(MapiHdl hdl, int *len, int fields, char more)
{
@@ -1461,9 +1460,9 @@ setFormatter(char *s)
formatter = TESTformatter;
} else if (strcmp(s, "timer") == 0) {
formatter = TIMERformatter;
- } else if (strcmp(s, "sam") == 0) {
- formatter = SAMformatter;
- } else {
+ } else if (strcmp(s, "sam") == 0) {
+ formatter = SAMformatter;
+ } else {
mnstr_printf(toConsole, "unsupported formatter\n");
}
}
@@ -1681,9 +1680,9 @@ format_result(Mapi mid, MapiHdl hdl, cha
case TIMERformatter:
TIMERrenderer(hdl);
break;
- case SAMformatter:
- SAMrenderer(hdl);
- break;
+ case SAMformatter:
+ SAMrenderer(hdl);
+ break;
default:
RAWrenderer(hdl);
break;
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2391,17 +2391,17 @@ AM_CONDITIONAL(HAVE_MSEED, test x"$have_
# samtools, only used by sql
have_samtools="auto"
AC_ARG_WITH(samtools,
- AS_HELP_STRING([--with-samtools=DIR],[samtools (providing bam library) are
installed in DIR]),
- [have_samtools="$withval"], [have_samtools="auto"])
+ 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$have_samtools/lib -lbam"
- ;;
+ SAMTOOLS_CFLAGS="-I$have_samtools/include"
+ SAMTOOLS_LIBS="-L$have_samtools/lib -lbam"
+ ;;
esac
save_CPPFLAGS="$CPPFLAGS"
@@ -2418,10 +2418,10 @@ if test "x$have_samtools" != xno; then
[ if test "x$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
+ 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)
diff --git a/sql/backends/monet5/bamloader/85_bam.mal
b/sql/backends/monet5/bamloader/85_bam.mal
--- a/sql/backends/monet5/bamloader/85_bam.mal
+++ b/sql/backends/monet5/bamloader/85_bam.mal
@@ -1,1 +1,1 @@
-include bam;
\ No newline at end of file
+include bam;
diff --git a/sql/backends/monet5/bamloader/Makefile.ag
b/sql/backends/monet5/bamloader/Makefile.ag
--- a/sql/backends/monet5/bamloader/Makefile.ag
+++ b/sql/backends/monet5/bamloader/Makefile.ag
@@ -18,7 +18,7 @@
INCLUDES = .. \
../../../include \
../../../common \
- ../../../storage \
+ ../../../storage \
../../../server \
../../../../monetdb5/modules/atoms \
../../../../monetdb5/modules/kernel \
diff --git a/sql/backends/monet5/bamloader/Tests/All
b/sql/backends/monet5/bamloader/Tests/All
--- a/sql/backends/monet5/bamloader/Tests/All
+++ b/sql/backends/monet5/bamloader/Tests/All
@@ -1,2 +1,2 @@
load
-benchmarks
\ No newline at end of file
+benchmarks
diff --git a/sql/backends/monet5/bamloader/Tests/benchmarks.py
b/sql/backends/monet5/bamloader/Tests/benchmarks.py
--- a/sql/backends/monet5/bamloader/Tests/benchmarks.py
+++ b/sql/backends/monet5/bamloader/Tests/benchmarks.py
@@ -1,1 +1,1 @@
-# generate output for all benchmarks
\ No newline at end of file
+# generate output for all benchmarks
diff --git a/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.1.sql
b/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.1.sql
--- a/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.1.sql
+++ b/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.1.sql
@@ -29,4 +29,4 @@ FROM (
WHERE bam_flag(flag, 'last_segm') = True
) AS r
ON l.qname = r.qname
-ORDER BY qname;
\ No newline at end of file
+ORDER BY qname;
diff --git a/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.8.sql
b/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.8.sql
--- a/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.8.sql
+++ b/sql/backends/monet5/bamloader/Tests/benchmarks_0/query2.8.sql
@@ -16,4 +16,4 @@ FROM (
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;
\ No newline at end of file
+ORDER BY qname;
diff --git a/sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.1.sql
b/sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.1.sql
--- a/sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.1.sql
+++ b/sql/backends/monet5/bamloader/Tests/benchmarks_1/query2.1.sql
@@ -6,4 +6,4 @@ SELECT qname,
FROM bam.paired_primary_alignments_i
WHERE l_mapq < mapq_2_1
AND r_mapq < mapq_2_1
-ORDER BY qname;
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