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 \ _______________________________________________ checkin-list mailing list checkin-list@monetdb.org https://www.monetdb.org/mailman/listinfo/checkin-list