Changeset: f4b5d5702d8b for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=f4b5d5702d8b
Added Files:
sql/backends/monet5/bam/bam_export.c
sql/backends/monet5/bam/bam_export.h
Modified Files:
sql/backends/monet5/bam/85_bam.sql
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/bam.mal
sql/backends/monet5/bam/bam_db_interface.h
sql/backends/monet5/bam/bam_loader.c
Branch: bamloader
Log Message:
Created framework for export functions
diffs (217 lines):
diff --git a/sql/backends/monet5/bam/85_bam.sql
b/sql/backends/monet5/bam/85_bam.sql
--- a/sql/backends/monet5/bam/85_bam.sql
+++ b/sql/backends/monet5/bam/85_bam.sql
@@ -22,3 +22,10 @@ RETURNS STRING EXTERNAL NAME bam.reverse
CREATE FUNCTION seq_length(cigar STRING)
RETURNS INT EXTERNAL NAME bam.seq_length;
+
+
+CREATE PROCEDURE sam_export(output_path STRING)
+EXTERNAL NAME bam.sam_export;
+
+CREATE PROCEDURE bam_export(output_path STRING)
+EXTERNAL NAME bam.bam_export;
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
@@ -36,7 +36,12 @@ INCLUDES = .. \
lib__bam = {
MODULE
DIR = libdir/monetdb5
- 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_lib.c bam_lib.h
+ 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_lib.c bam_lib.h \
+ bam_export.c bam_export.h
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
../../../../gdk/libbat \
$(SAMTOOLS_LIBS)
diff --git a/sql/backends/monet5/bam/bam.mal b/sql/backends/monet5/bam/bam.mal
--- a/sql/backends/monet5/bam/bam.mal
+++ b/sql/backends/monet5/bam/bam.mal
@@ -39,6 +39,17 @@ address seq_length_bat
comment "Calculate the real length of a DNA sequence, given its CIGAR string."
+# Export signatures
+
+pattern sam_export(output_path:str):void
+address sam_export
+comment "Export results in the bam.export table to a SAM file"
+
+pattern bam_export(output_path:str):void
+address bam_export
+comment "Export results in the bam.export table to a BAM file"
+
+
# BAT signatures for bam_lib
module batbam;
diff --git a/sql/backends/monet5/bam/bam_db_interface.h
b/sql/backends/monet5/bam/bam_db_interface.h
--- a/sql/backends/monet5/bam/bam_db_interface.h
+++ b/sql/backends/monet5/bam/bam_db_interface.h
@@ -108,6 +108,20 @@
CONSTRAINT pg_fkey_file_id FOREIGN KEY (file_id) REFERENCES bam.files
(file_id) \n\
);"
+#define SQL_CREATE_EXPORT \
+ "CREATE TABLE bam.export ( \n\
+ qname STRING NOT NULL, \n\
+ flag SMALLINT NOT NULL, \n\
+ rname STRING NOT NULL, \n\
+ pos INT NOT NULL, \n\
+ mapq SMALLINT NOT NULL, \n\
+ cigar STRING NOT NULL, \n\
+ rnext STRING NOT NULL, \n\
+ pnext INT NOT NULL, \n\
+ tlen INT NOT NULL, \n\
+ seq STRING NOT NULL, \n\
+ qual STRING NOT NULL \n\
+ );"
str create_schema_if_not_exists(Client cntxt, mvc * m, str schemaname,
str descr, sql_schema ** ret);
diff --git a/sql/backends/monet5/bam/bam_export.c
b/sql/backends/monet5/bam/bam_export.c
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/bam_export.c
@@ -0,0 +1,60 @@
+/*
+ * 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
+ * The code in this file defines export functionality, that enables
+ * users to write data from the bam.export table to a SAM or BAM file.
+ * After exporting data, the exporting functions will automatically
+ * empty the bam.export table.
+ */
+
+#include "monetdb_config.h"
+#include "bam_export.h"
+
+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;
+ (void)stk;
+ (void)pci;
+ throw(MAL, "sam_export", "Not implemented yet...");
+}
+
+
+
+str
+bam_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;
+ (void)stk;
+ (void)pci;
+ throw(MAL, "bam_export", "Not implemented yet...");
+}
+
diff --git a/sql/backends/monet5/bam/bam_export.h
b/sql/backends/monet5/bam/bam_export.h
new file mode 100644
--- /dev/null
+++ b/sql/backends/monet5/bam/bam_export.h
@@ -0,0 +1,55 @@
+/*
+ * 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
+ * The code in this file defines export functionality, that enables
+ * users to write data from the bam.export table to a SAM or BAM file.
+ * After exporting data, the exporting functions will automatically
+ * empty the bam.export table.
+ */
+
+#ifndef _BAM_EXPORT_H
+#define _BAM_EXPORT_H
+
+#include "sql_scenario.h"
+#include "sql_mvc.h"
+
+
+/* Note: Unlike in the other BAM source files, we use bam_exp instead of
+ * bam_export here, since bam_export is a used function name in this file */
+#ifdef WIN32
+#ifndef LIBBAM
+#define bam_exp extern __declspec(dllimport)
+#else
+#define bam_exp extern __declspec(dllexport)
+#endif
+#else
+#define bam_exp extern
+#endif
+
+
+bam_exp str sam_export(Client cntxt, MalBlkPtr mb, MalStkPtr stk,
+ InstrPtr pci);
+bam_exp str bam_export(Client cntxt, MalBlkPtr mb, MalStkPtr stk,
+ InstrPtr pci);
+
+
+
+#endif
diff --git a/sql/backends/monet5/bam/bam_loader.c
b/sql/backends/monet5/bam/bam_loader.c
--- a/sql/backends/monet5/bam/bam_loader.c
+++ b/sql/backends/monet5/bam/bam_loader.c
@@ -247,6 +247,12 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
"bam.create_pg",
NULL)) != MAL_SUCCEED)
goto cleanup;
+
+ if ((msg =
+ create_table_if_not_exists(cntxt, m, s, "export",
SQL_CREATE_EXPORT,
+ "bam.create_export",
+ NULL)) != MAL_SUCCEED)
+ goto cleanup;
/* Get next file id */
TO_LOG("<bam_loader> Retrieving next file id...\n");
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