Changeset: aeed76d1d22e for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=aeed76d1d22e
Modified Files:
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/bam_db_interface.c
sql/backends/monet5/bam/bam_db_interface.h
sql/backends/monet5/bam/bam_export.c
sql/backends/monet5/bam/bam_export.h
sql/backends/monet5/bam/bam_globals.h
sql/backends/monet5/bam/bam_lib.c
sql/backends/monet5/bam/bam_loader.c
sql/backends/monet5/bam/bam_loader.h
sql/backends/monet5/bam/bam_wrapper.c
sql/backends/monet5/bam/bam_wrapper.h
Branch: bamloader
Log Message:
Fixed indentation (spaces to tabs) and removed whitespace at the end of lines
diffs (truncated from 4809 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
@@ -37,14 +37,14 @@ 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.c bam_globals.h \
- bam_lib.c bam_lib.h \
- bam_export.c bam_export.h
+ bam_wrapper.c bam_wrapper.h \
+ bam_db_interface.c bam_db_interface.h \
+ bam_globals.c bam_globals.h \
+ bam_lib.c bam_lib.h \
+ bam_export.c bam_export.h
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
- ../../../../gdk/libbat \
- $(SAMTOOLS_LIBS)
+ ../../../../gdk/libbat \
+ $(SAMTOOLS_LIBS)
}
headers_mal = {
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
@@ -28,172 +28,172 @@
#include "bam_db_interface.h"
#define SQL_CREATE_STORAGE_0 \
- "CREATE TABLE bam.alignments_"LLFMT" ( \n\
- virtual_offset BIGINT NOT NULL, \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\
- CONSTRAINT alignments_"LLFMT"_pkey_virtual_offset PRIMARY KEY
(virtual_offset) \n\
- ); \n\
- \n\
- CREATE TABLE bam.alignments_extra_"LLFMT" ( \n\
- tag CHAR(2) NOT NULL, \n\
- virtual_offset BIGINT NOT NULL, \n\
- type CHAR(1) NOT NULL, \n\
- value STRING, \n\
- CONSTRAINT alignments_extra_"LLFMT"_pkey_tag_virtual_offset PRIMARY
KEY (tag, virtual_offset), \n\
- CONSTRAINT alignments_extra_"LLFMT"_fkey_virtual_offset FOREIGN KEY
(virtual_offset) \n\
- REFERENCES bam.alignments_"LLFMT" (virtual_offset) \n\
- );"
+ "CREATE TABLE bam.alignments_"LLFMT" ( \n\
+ virtual_offset BIGINT NOT NULL, \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\
+ CONSTRAINT alignments_"LLFMT"_pkey_virtual_offset PRIMARY KEY
(virtual_offset) \n\
+ ); \n\
+ \n\
+ CREATE TABLE bam.alignments_extra_"LLFMT" ( \n\
+ tag CHAR(2)
NOT NULL, \n\
+ virtual_offset BIGINT NOT NULL, \n\
+ type CHAR(1)
NOT NULL, \n\
+ value STRING, \n\
+ CONSTRAINT alignments_extra_"LLFMT"_pkey_tag_virtual_offset
PRIMARY KEY (tag, virtual_offset), \n\
+ CONSTRAINT alignments_extra_"LLFMT"_fkey_virtual_offset FOREIGN
KEY (virtual_offset) \n\
+ REFERENCES bam.alignments_"LLFMT" (virtual_offset) \n\
+ );"
#define SQL_CREATE_STORAGE_1 \
- "CREATE TABLE bam.paired_primary_alignments_"LLFMT" ( \n\
- l_virtual_offset BIGINT NOT NULL, \n\
- r_virtual_offset BIGINT NOT NULL, \n\
- qname STRING NOT NULL, \n\
- l_flag SMALLINT NOT NULL, \n\
- l_rname STRING NOT NULL, \n\
- l_pos INT NOT NULL, \n\
- l_mapq SMALLINT NOT NULL, \n\
- l_cigar STRING NOT NULL, \n\
- l_rnext STRING NOT NULL, \n\
- l_pnext INT NOT NULL, \n\
- l_tlen INT NOT NULL, \n\
- l_seq STRING NOT NULL, \n\
- l_qual STRING NOT NULL, \n\
- r_flag SMALLINT NOT NULL, \n\
- r_rname STRING NOT NULL, \n\
- r_pos INT NOT NULL, \n\
- r_mapq SMALLINT NOT NULL, \n\
- r_cigar STRING NOT NULL, \n\
- r_rnext STRING NOT NULL, \n\
- r_pnext INT NOT NULL, \n\
- r_tlen INT NOT NULL, \n\
- r_seq STRING NOT NULL, \n\
- r_qual STRING NOT NULL, \n\
- CONSTRAINT
paired_primary_alignments_"LLFMT"_pkey_l_virtual_offset_r_virtual_offset \n\
- PRIMARY KEY (l_virtual_offset, r_virtual_offset) \n\
- ); \n\
- \n\
- CREATE TABLE bam.paired_secondary_alignments_"LLFMT" ( \n\
- l_virtual_offset BIGINT NOT NULL, \n\
- r_virtual_offset BIGINT NOT NULL, \n\
- qname STRING NOT NULL, \n\
- l_flag SMALLINT NOT NULL, \n\
- l_rname STRING NOT NULL, \n\
- l_pos INT NOT NULL, \n\
- l_mapq SMALLINT NOT NULL, \n\
- l_cigar STRING NOT NULL, \n\
- l_rnext STRING NOT NULL, \n\
- l_pnext INT NOT NULL, \n\
- l_tlen INT NOT NULL, \n\
- l_seq STRING NOT NULL, \n\
- l_qual STRING NOT NULL, \n\
- r_flag SMALLINT NOT NULL, \n\
- r_rname STRING NOT NULL, \n\
- r_pos INT NOT NULL, \n\
- r_mapq SMALLINT NOT NULL, \n\
- r_cigar STRING NOT NULL, \n\
- r_rnext STRING NOT NULL, \n\
- r_pnext INT NOT NULL, \n\
- r_tlen INT NOT NULL, \n\
- r_seq STRING NOT NULL, \n\
- r_qual STRING NOT NULL, \n\
- CONSTRAINT
paired_secondary_alignments_"LLFMT"_pkey_l_virtual_offset_r_virtual_offset \n\
- PRIMARY KEY (l_virtual_offset, r_virtual_offset) \n\
- ); \n\
- \n\
- CREATE TABLE bam.unpaired_alignments_"LLFMT" ( \n\
- virtual_offset BIGINT NOT NULL, \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\
- CONSTRAINT unpaired_alignments_"LLFMT"_pkey_virtual_offset PRIMARY KEY
(virtual_offset) \n\
- ); \n\
- \n\
- CREATE TABLE bam.alignments_extra_"LLFMT" ( \n\
- tag CHAR(2) NOT NULL, \n\
- virtual_offset BIGINT NOT NULL, \n\
- type CHAR(1) NOT NULL, \n\
- value STRING, \n\
- CONSTRAINT alignments_extra_"LLFMT"_pkey_tag_virtual_offset PRIMARY KEY
(tag, virtual_offset) \n\
- ); \n\
- \n\
- CREATE VIEW bam.unpaired_primary_alignments_"LLFMT" AS \n\
- SELECT l_virtual_offset AS virtual_offset, qname, l_flag AS flag,
l_rname AS rname, l_pos AS pos, l_mapq AS mapq, \n\
- l_cigar AS cigar, l_rnext AS rnext, l_pnext AS pnext, l_tlen AS
tlen, l_seq AS seq, l_qual AS qual \n\
- FROM bam.paired_primary_alignments_"LLFMT" \n\
- UNION ALL \n\
- SELECT r_virtual_offset AS virtual_offset, qname, r_flag AS flag,
r_rname AS rname, r_pos AS pos, r_mapq AS mapq, \n\
- r_cigar AS cigar, r_rnext AS rnext, r_pnext AS pnext, r_tlen AS
tlen, r_seq AS seq, r_qual AS qual \n\
- FROM bam.paired_primary_alignments_"LLFMT"; \n\
- \n\
- CREATE VIEW bam.unpaired_secondary_alignments_"LLFMT" AS \n\
- SELECT l_virtual_offset AS virtual_offset, qname, l_flag AS flag,
l_rname AS rname, l_pos AS pos, l_mapq AS mapq, \n\
- l_cigar AS cigar, l_rnext AS rnext, l_pnext AS pnext, l_tlen AS
tlen, l_seq AS seq, l_qual AS qual \n\
- FROM bam.paired_secondary_alignments_"LLFMT" \n\
- UNION ALL \n\
- SELECT r_virtual_offset AS virtual_offset, qname, r_flag AS flag,
r_rname AS rname, r_pos AS pos, r_mapq AS mapq, \n\
- r_cigar AS cigar, r_rnext AS rnext, r_pnext AS pnext, r_tlen AS
tlen, r_seq AS seq, r_qual AS qual \n\
- FROM bam.paired_secondary_alignments_"LLFMT"; \n\
- \n\
- CREATE VIEW bam.unpaired_all_alignments_"LLFMT" AS \n\
- SELECT * \n\
- FROM bam.unpaired_primary_alignments_"LLFMT" \n\
- UNION ALL \n\
- SELECT * \n\
- FROM bam.unpaired_secondary_alignments_"LLFMT" \n\
- UNION ALL \n\
- SELECT * \n\
- FROM bam.unpaired_alignments_"LLFMT";"
+ "CREATE TABLE bam.paired_primary_alignments_"LLFMT" ( \n\
+ l_virtual_offset BIGINT NOT
NULL, \n\
+ r_virtual_offset BIGINT NOT
NULL, \n\
+ qname STRING NOT
NULL, \n\
+ l_flag SMALLINT
NOT NULL, \n\
+ l_rname STRING NOT
NULL, \n\
+ l_pos INT
NOT NULL, \n\
+ l_mapq SMALLINT
NOT NULL, \n\
+ l_cigar STRING NOT
NULL, \n\
+ l_rnext STRING NOT
NULL, \n\
+ l_pnext INT NOT
NULL, \n\
+ l_tlen INT
NOT NULL, \n\
+ l_seq STRING NOT
NULL, \n\
+ l_qual STRING NOT
NULL, \n\
+ r_flag SMALLINT
NOT NULL, \n\
+ r_rname STRING NOT
NULL, \n\
+ r_pos INT
NOT NULL, \n\
+ r_mapq SMALLINT
NOT NULL, \n\
+ r_cigar STRING NOT
NULL, \n\
+ r_rnext STRING NOT
NULL, \n\
+ r_pnext INT NOT
NULL, \n\
+ r_tlen INT
NOT NULL, \n\
+ r_seq STRING NOT
NULL, \n\
+ r_qual STRING NOT
NULL, \n\
+ CONSTRAINT
paired_primary_alignments_"LLFMT"_pkey_l_virtual_offset_r_virtual_offset \n\
+ PRIMARY KEY (l_virtual_offset, r_virtual_offset) \n\
+ ); \n\
+ \n\
+ CREATE TABLE bam.paired_secondary_alignments_"LLFMT" ( \n\
+ l_virtual_offset BIGINT NOT
NULL, \n\
+ r_virtual_offset BIGINT NOT
NULL, \n\
+ qname STRING NOT
NULL, \n\
+ l_flag SMALLINT
NOT NULL, \n\
+ l_rname STRING NOT
NULL, \n\
+ l_pos INT
NOT NULL, \n\
+ l_mapq SMALLINT
NOT NULL, \n\
+ l_cigar STRING NOT
NULL, \n\
+ l_rnext STRING NOT
NULL, \n\
+ l_pnext INT NOT
NULL, \n\
+ l_tlen INT
NOT NULL, \n\
+ l_seq STRING NOT
NULL, \n\
+ l_qual STRING NOT
NULL, \n\
+ r_flag SMALLINT
NOT NULL, \n\
+ r_rname STRING NOT
NULL, \n\
+ r_pos INT
NOT NULL, \n\
+ r_mapq SMALLINT
NOT NULL, \n\
+ r_cigar STRING NOT
NULL, \n\
+ r_rnext STRING NOT
NULL, \n\
+ r_pnext INT NOT
NULL, \n\
+ r_tlen INT
NOT NULL, \n\
+ r_seq STRING NOT
NULL, \n\
+ r_qual STRING NOT
NULL, \n\
+ CONSTRAINT
paired_secondary_alignments_"LLFMT"_pkey_l_virtual_offset_r_virtual_offset \n\
+ PRIMARY KEY (l_virtual_offset, r_virtual_offset) \n\
+ ); \n\
+ \n\
+ CREATE TABLE bam.unpaired_alignments_"LLFMT" ( \n\
+ virtual_offset BIGINT NOT NULL, \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\
+ CONSTRAINT unpaired_alignments_"LLFMT"_pkey_virtual_offset
PRIMARY KEY (virtual_offset) \n\
+ ); \n\
+ \n\
+ CREATE TABLE bam.alignments_extra_"LLFMT" ( \n\
+ tag CHAR(2) NOT
NULL, \n\
+ virtual_offset BIGINT NOT NULL, \n\
+ type CHAR(1) NOT
NULL, \n\
+ value STRING, \n\
+ CONSTRAINT alignments_extra_"LLFMT"_pkey_tag_virtual_offset PRIMARY KEY
(tag, virtual_offset) \n\
+ ); \n\
+ \n\
+ CREATE VIEW bam.unpaired_primary_alignments_"LLFMT" AS \n\
+ SELECT l_virtual_offset AS virtual_offset, qname, l_flag AS
flag, l_rname AS rname, l_pos AS pos, l_mapq AS mapq, \n\
+ l_cigar AS cigar, l_rnext AS rnext, l_pnext AS pnext,
l_tlen AS tlen, l_seq AS seq, l_qual AS qual \n\
+ FROM bam.paired_primary_alignments_"LLFMT" \n\
+ UNION ALL \n\
+ SELECT r_virtual_offset AS virtual_offset, qname, r_flag AS
flag, r_rname AS rname, r_pos AS pos, r_mapq AS mapq, \n\
+ r_cigar AS cigar, r_rnext AS rnext, r_pnext AS pnext,
r_tlen AS tlen, r_seq AS seq, r_qual AS qual \n\
+ FROM bam.paired_primary_alignments_"LLFMT"; \n\
+ \n\
+ CREATE VIEW bam.unpaired_secondary_alignments_"LLFMT" AS \n\
+ SELECT l_virtual_offset AS virtual_offset, qname, l_flag AS
flag, l_rname AS rname, l_pos AS pos, l_mapq AS mapq, \n\
+ l_cigar AS cigar, l_rnext AS rnext, l_pnext AS pnext,
l_tlen AS tlen, l_seq AS seq, l_qual AS qual \n\
+ FROM bam.paired_secondary_alignments_"LLFMT" \n\
+ UNION ALL \n\
+ SELECT r_virtual_offset AS virtual_offset, qname, r_flag AS
flag, r_rname AS rname, r_pos AS pos, r_mapq AS mapq, \n\
+ r_cigar AS cigar, r_rnext AS rnext, r_pnext AS pnext,
r_tlen AS tlen, r_seq AS seq, r_qual AS qual \n\
+ FROM bam.paired_secondary_alignments_"LLFMT"; \n\
+ \n\
+ CREATE VIEW bam.unpaired_all_alignments_"LLFMT" AS \n\
+ SELECT * \n\
+ FROM bam.unpaired_primary_alignments_"LLFMT" \n\
+ UNION ALL \n\
+ SELECT * \n\
+ FROM bam.unpaired_secondary_alignments_"LLFMT" \n\
+ UNION ALL \n\
+ SELECT * \n\
+ FROM bam.unpaired_alignments_"LLFMT";"
#define SQL_DROP_HEADER \
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