Changeset: 26e61351bc15 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=26e61351bc15
Added Files:
sql/backends/monet5/bam/bam_globals.c
Modified Files:
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/bam_db_interface.c
sql/backends/monet5/bam/bam_export.c
sql/backends/monet5/bam/bam_globals.h
sql/backends/monet5/bam/bam_wrapper.c
sql/backends/monet5/bam/bam_wrapper.h
Branch: bamloader
Log Message:
Implemented sam_export function.
diffs (truncated from 318 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
@@ -39,7 +39,7 @@ lib__bam = {
SOURCES = bam_loader.c bam_loader.h \
bam_wrapper.c bam_wrapper.h \
bam_db_interface.c bam_db_interface.h \
- bam_globals.h \
+ bam_globals.c bam_globals.h \
bam_lib.c bam_lib.h \
bam_export.c bam_export.h
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
diff --git a/sql/backends/monet5/bam/bam_db_interface.c
b/sql/backends/monet5/bam/bam_db_interface.c
--- a/sql/backends/monet5/bam/bam_db_interface.c
+++ b/sql/backends/monet5/bam/bam_db_interface.c
@@ -297,7 +297,6 @@ next_file_id(mvc * m, sql_table * files,
sql_column *c;
BAT *b = NULL;
BATiter li;
- sht i;
BUN p = 0, q = 0;
lng max_file_id = 0;
@@ -310,20 +309,16 @@ next_file_id(mvc * m, sql_table * files,
"Could not retrieve the next file id: Error binding
file_id column of 'files' table");
}
- /* Loop through all BATs for this column, i.e. the real BAT
- * and the delta BATs and find the maximum file_id */
- for (i = 0; i < 3; ++i) {
- b = store_funcs.bind_col(m->session->tr, c, i);
- if (b != NULL) {
- li = bat_iterator(b);
- BATloop(b, p, q) {
- lng t = *(lng *) BUNtail(li, p);
+ /* Loop through BAT for this column and find the maximum file_id */
+ b = store_funcs.bind_col(m->session->tr, c, RD_INS);
- max_file_id = MAX(max_file_id, t);
- }
- BBPreleaseref(b->batCacheid);
- }
- }
+ li = bat_iterator(b);
+ BATloop(b, p, q) {
+ lng t = *(lng *) BUNtail(li, p);
+ max_file_id = MAX(max_file_id, t);
+ }
+ BBPreleaseref(b->batCacheid);
+
*next_file_id = max_file_id + 1;
return MAL_SUCCEED;
}
diff --git a/sql/backends/monet5/bam/bam_export.c
b/sql/backends/monet5/bam/bam_export.c
--- a/sql/backends/monet5/bam/bam_export.c
+++ b/sql/backends/monet5/bam/bam_export.c
@@ -26,20 +26,133 @@
*/
#include "monetdb_config.h"
+
+#include "bam_globals.h"
#include "bam_export.h"
+
+typedef struct bam_field {
+ str name;
+ sql_column *c;
+ BAT *b;
+ BATiter iter;
+ BUN cur;
+} bam_field;
+
+
+#define CUR_STR(field, i) ((str) BUNtail(field.iter, (field.cur+i)))
+#define CUR_SHT(field, i) (*(sht *) BUNtail(field.iter, (field.cur+i)))
+#define CUR_INT(field, i) (*(int *) BUNtail(field.iter, (field.cur+i)))
+
str
sam_export(Client cntxt, MalBlkPtr mb, MalStkPtr stk, InstrPtr pci)
{
/* arg 1: path to desired output file */
str output_path = *(str *) getArgReference(stk, pci, pci->retc);
-
- (void)output_path;
- (void)cntxt;
- (void)mb;
+
+ mvc *m;
+ sql_schema *s_bam;
+ sql_table *t_export;
+ bam_field fields[11];
+
+ stream *output = NULL;
+
+ int cnt, i;
+ str msg = MAL_SUCCEED;
+
+ memset(fields, 0, 11 * sizeof(bam_field));
+
+ if ((output = bsopen(output_path)) == NULL) {
+ msg = createException(MAL, "sam_export", "Could not open output file
'%s' for writing", output_path);
+ goto cleanup;
+ }
+
+ if ((msg = getSQLContext(cntxt, mb, &m, NULL)) != MAL_SUCCEED) {
+ REUSE_EXCEPTION(msg, MAL, "sam_export", "Could not retrieve SQL
context: %s", msg);
+ goto cleanup;
+ }
+
+ if ((s_bam = mvc_bind_schema(m, "bam")) == NULL) {
+ msg = createException(MAL, "sam_export", "Could not find bam schema");
+ goto cleanup;
+ }
+
+ if ((t_export = mvc_bind_table(m, s_bam, "export")) == NULL) {
+ msg = createException(MAL, "sam_export", "Could not find bam.export
table");
+ goto cleanup;
+ }
+
+ fields[0].name = "qname";
+ fields[1].name = "flag";
+ fields[2].name = "rname";
+ fields[3].name = "pos";
+ fields[4].name = "mapq";
+ fields[5].name = "cigar";
+ fields[6].name = "rnext";
+ fields[7].name = "pnext";
+ fields[8].name = "tlen";
+ fields[9].name = "seq";
+ fields[10].name = "qual";
+
+ for (i=0; i<11; ++i) {
+ int cnt_tmp;
+ if ((fields[i].c = mvc_bind_column(m, t_export, fields[i].name)) ==
NULL) {
+ msg = createException(MAL, "sam_export", "Could not find
bam.export.%s column", fields[i].name);
+ goto cleanup;
+ }
+ if ((fields[i].b = store_funcs.bind_col(m->session->tr, fields[i].c,
RDONLY)) == NULL) {
+ msg = createException(MAL, "sam_export", RUNTIME_OBJECT_MISSING);
+ goto cleanup;
+ }
+ cnt_tmp = BATcount(fields[i].b);
+ if (cnt_tmp <= 0) {
+ msg = createException(MAL, "sam_export", "The bam.export table is
empty");
+ goto cleanup;
+ }
+ if (i > 0 && cnt != cnt_tmp) {
+ msg = createException(MAL, "sam_export", "Misalignment in
bam.export table: "
+ "column '%s' has %d values; expected %d",
+ fields[i].name, cnt_tmp, cnt);
+ goto cleanup;
+ }
+ cnt = cnt_tmp;
+ fields[i].iter = bat_iterator(fields[i].b);
+ fields[i].cur = BUNfirst(fields[i].b);
+ }
+
+ /* Build header */
+ mnstr_printf(output, "@HD VN:1.0 SO:%s\n",
+ BATtordered(fields[0].b) ? "queryname" :
+ (BATordered(fields[2].b) && BATordered(fields[3].b) ?
"coordinate" :
+ "unsorted"));
+
+ /* TODO: Build SQ tags */
+
+ mnstr_printf(output, "@CO SAM file generated by MonetDB\n");
+
+
+ for (i=0; i<cnt; ++i) {
+ mnstr_printf(output, "%s\t%d\t%s\t%d\t%d\t%s\t%s\t%d\t%d\t%s\t%s\n",
+ CUR_STR(fields[0], i), CUR_SHT(fields[1], i),
CUR_STR(fields[2], i),
+ CUR_INT(fields[3], i), CUR_SHT(fields[4], i),
CUR_STR(fields[5], i),
+ CUR_STR(fields[6], i), CUR_INT(fields[7], i),
CUR_INT(fields[8], i),
+ CUR_STR(fields[9], i), CUR_STR(fields[10], i));
+ }
+
(void)stk;
(void)pci;
- throw(MAL, "sam_export", "Not implemented yet...");
+
+cleanup:
+ for (i=0; i<11; ++i) {
+ if (fields[i].b != NULL) {
+ BBPreleaseref(fields[i].b->batCacheid);
+ }
+ }
+ if (output) {
+ close_stream(output);
+ }
+
+ return msg;
}
diff --git a/sql/backends/monet5/bam/bam_globals.c
b/sql/backends/monet5/bam/bam_globals.c
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/bam_globals.c
@@ -0,0 +1,51 @@
+/*
+ * The contents of this file are subject to the MonetDB Public License
+ * Version 1.1 (the "License"); you may not use this file except in
+ * compliance with the License. You may obtain a copy of the License at
+ * http://www.monetdb.org/Legal/MonetDBLicense
+ *
+ * Software distributed under the License is distributed on an "AS IS"
+ * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+ * License for the specific language governing rights and limitations
+ * under the License.
+ *
+ * The Original Code is the MonetDB Database System.
+ *
+ * The Initial Developer of the Original Code is CWI.
+ * Portions created by CWI are Copyright (C) 1997-July 2008 CWI.
+ * Copyright August 2008-2014 MonetDB B.V.
+ * All Rights Reserved.
+ */
+
+/*
+ * (author) R Cijvat
+ * This file contains some global definitions, used by multiple bam
+ * library files
+ */
+
+
+
+
+#include "monetdb_config.h"
+
+#include "bam_globals.h"
+
+stream *
+bsopen(str filepath)
+{
+ stream *s;
+ stream *wbs;
+
+ if ((s = open_wastream(filepath)) == NULL) {
+ return NULL;
+ }
+ if (mnstr_errnr(s)) {
+ close_stream(s);
+ return NULL;
+ }
+ if ((wbs = wbstream(s, BSTREAM_CHUNK_SIZE)) == NULL) {
+ close_stream(s);
+ return NULL;
+ }
+ return wbs;
+}
\ No newline at end of file
diff --git a/sql/backends/monet5/bam/bam_globals.h
b/sql/backends/monet5/bam/bam_globals.h
--- a/sql/backends/monet5/bam/bam_globals.h
+++ b/sql/backends/monet5/bam/bam_globals.h
@@ -28,6 +28,7 @@
#include <string.h>
#include "gdk.h"
+#include "stream.h"
@@ -109,5 +110,13 @@ hash_fprintf(FILE *f, const char *format
GDKfree(msg); \
msg = msg_tmp; \
} while (0)
+
+
+
+#define BSTREAM_CHUNK_SIZE BUFSIZ
+
+
+stream *
+bsopen(str filepath);
#endif
diff --git a/sql/backends/monet5/bam/bam_wrapper.c
b/sql/backends/monet5/bam/bam_wrapper.c
--- a/sql/backends/monet5/bam/bam_wrapper.c
+++ b/sql/backends/monet5/bam/bam_wrapper.c
@@ -63,26 +63,6 @@ get_ordering(str ord)
return ORDERING_UNKNOWN;
}
-static stream *
-bsopen(str filepath)
-{
- stream *s;
- stream *wbs;
-
- if ((s = open_wastream(filepath)) == NULL) {
- return NULL;
- }
- if (mnstr_errnr(s)) {
- close_stream(s);
- return NULL;
- }
- if ((wbs = wbstream(s, BSTREAM_CHUNK_SIZE)) == NULL) {
- close_stream(s);
- return NULL;
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