Commit 3c60782c authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

Applying schema patch for bamcov support.

parent 12f9bd76
......@@ -24,6 +24,7 @@
80 \N patch patch_77_78_b.sql|source_column_increase
81 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
82 \N patch patch_78_79_a.sql|schema_version
83 \N patch patch_78_79_b.sql|bamcov support
1 \N schema_type core
2 \N schema_version 79
8 1 assembly.accession GCA_000292705.1
......
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -469,7 +469,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=InnoDB AUTO_INCREMENT=83 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=84 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
......@@ -59,3 +59,4 @@
119 \N patch patch_77_78_b.sql|source_column_increase
120 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
121 \N patch patch_78_79_a.sql|schema_version
122 \N patch patch_78_79_b.sql|bamcov support
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -266,7 +266,7 @@ CREATE TABLE `external_db` (
`description` text,
PRIMARY KEY (`external_db_id`),
UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
) ENGINE=MyISAM AUTO_INCREMENT=4201 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=11001 DEFAULT CHARSET=latin1;
CREATE TABLE `external_synonym` (
`xref_id` int(10) unsigned NOT NULL,
......@@ -468,7 +468,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=122 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=123 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
......@@ -59,3 +59,4 @@
108 \N patch patch_77_78_b.sql|source_column_increase
109 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
110 \N patch patch_78_79_a.sql|schema_version
111 \N patch patch_78_79_b.sql|bamcov support
......@@ -127,7 +127,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -463,7 +463,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=111 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=112 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL DEFAULT '',
......
......@@ -64,3 +64,4 @@
2071 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
2072 \N patch patch_78_79_a.sql|schema_version
2073 \N patch patch_73_74_h.sql|alt_allele_unique_gene_idx
2074 \N patch patch_78_79_b.sql|bamcov support
......@@ -104,7 +104,7 @@ CREATE TABLE `attrib_type` (
`description` text COLLATE latin1_bin,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `c` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=397 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=405 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -127,7 +127,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -144,7 +144,7 @@ CREATE TABLE `density_feature` (
PRIMARY KEY (`density_feature_id`),
KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
KEY `seq_region_id_idx` (`seq_region_id`)
) ENGINE=MyISAM AUTO_INCREMENT=16758814 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=16758826 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `density_type` (
`density_type_id` int(11) NOT NULL AUTO_INCREMENT,
......@@ -154,7 +154,7 @@ CREATE TABLE `density_type` (
`value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=MyISAM AUTO_INCREMENT=102 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
) ENGINE=MyISAM AUTO_INCREMENT=110 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
......@@ -332,7 +332,7 @@ CREATE TABLE `genome_statistics` (
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -463,7 +463,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=2074 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2075 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......
......@@ -20,3 +20,4 @@
113 \N patch patch_77_78_b.sql|source_column_increase
114 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
115 \N patch patch_78_79_a.sql|schema_version
116 \N patch patch_78_79_b.sql|bamcov support
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -468,7 +468,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=116 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=117 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
......@@ -58,3 +58,4 @@
112 \N patch patch_77_78_b.sql|source_column_increase
113 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
114 \N patch patch_78_79_a.sql|schema_version
115 \N patch patch_78_79_b.sql|bamcov support
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -468,7 +468,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=115 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=116 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
......@@ -113,3 +113,4 @@
193 \N patch patch_77_78_b.sql|source_column_increase
194 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
195 \N patch patch_78_79_a.sql|schema_version
196 \N patch patch_78_79_b.sql|bamcov support
......@@ -103,7 +103,7 @@ CREATE TABLE `attrib_type` (
`description` text,
PRIMARY KEY (`attrib_type_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=20 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=437 DEFAULT CHARSET=latin1;
CREATE TABLE `coord_system` (
`coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -116,7 +116,7 @@ CREATE TABLE `coord_system` (
UNIQUE KEY `rank_idx` (`rank`,`species_id`),
UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
KEY `species_idx` (`species_id`)
) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
CREATE TABLE `data_file` (
`data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -153,7 +153,7 @@ CREATE TABLE `density_type` (
`value_type` enum('sum','ratio') NOT NULL,
PRIMARY KEY (`density_type_id`),
UNIQUE KEY `analysis_idx` (`analysis_id`,`block_size`,`region_features`)
) ENGINE=MyISAM AUTO_INCREMENT=7 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1;
CREATE TABLE `dependent_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
......@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
PRIMARY KEY (`exon_id`),
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=162051 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=382467 DEFAULT CHARSET=latin1;
CREATE TABLE `exon_transcript` (
`exon_id` int(10) unsigned NOT NULL,
......@@ -299,7 +299,7 @@ CREATE TABLE `gene` (
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`),
KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
) ENGINE=MyISAM AUTO_INCREMENT=18284 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=40234 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_archive` (
`gene_stable_id` varchar(128) NOT NULL,
......@@ -336,7 +336,7 @@ CREATE TABLE `genome_statistics` (
PRIMARY KEY (`genome_statistics_id`),
UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
CREATE TABLE `identity_xref` (
`object_xref_id` int(10) unsigned NOT NULL,
......@@ -468,7 +468,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=122 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=197 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -512,7 +512,7 @@ CREATE TABLE `misc_set` (
`max_length` int(10) unsigned NOT NULL,
PRIMARY KEY (`misc_set_id`),
UNIQUE KEY `code_idx` (`code`)
) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=24 DEFAULT CHARSET=latin1;
CREATE TABLE `object_xref` (
`object_xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -658,7 +658,7 @@ CREATE TABLE `protein_feature` (
KEY `analysis_idx` (`analysis_id`),
KEY `translation_idx` (`translation_id`),
KEY `hitname_idx` (`hit_name`)
) ENGINE=MyISAM AUTO_INCREMENT=242848 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=3502933 DEFAULT CHARSET=latin1;
CREATE TABLE `repeat_consensus` (
`repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -671,7 +671,7 @@ CREATE TABLE `repeat_consensus` (
KEY `class` (`repeat_class`),
KEY `consensus` (`repeat_consensus`(10)),
KEY `type` (`repeat_type`)
) ENGINE=MyISAM AUTO_INCREMENT=1020 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=1163919 DEFAULT CHARSET=latin1;
CREATE TABLE `repeat_feature` (
`repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -688,7 +688,7 @@ CREATE TABLE `repeat_feature` (
KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
KEY `repeat_idx` (`repeat_consensus_id`),
KEY `analysis_idx` (`analysis_id`)
) ENGINE=MyISAM AUTO_INCREMENT=922516 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
) ENGINE=MyISAM AUTO_INCREMENT=10446798 DEFAULT CHARSET=latin1 MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
CREATE TABLE `seq_region` (
`seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -698,7 +698,7 @@ CREATE TABLE `seq_region` (
PRIMARY KEY (`seq_region_id`),
UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
KEY `cs_idx` (`coord_system_id`)
) ENGINE=MyISAM AUTO_INCREMENT=965911 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=3495795 DEFAULT CHARSET=latin1;
CREATE TABLE `seq_region_attrib` (
`seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -789,7 +789,7 @@ CREATE TABLE `transcript` (
KEY `xref_id_index` (`display_xref_id`),
KEY `analysis_idx` (`analysis_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=21752 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
CREATE TABLE `transcript_attrib` (
`transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -832,7 +832,7 @@ CREATE TABLE `translation` (
PRIMARY KEY (`translation_id`),
KEY `transcript_idx` (`transcript_id`),
KEY `stable_id_idx` (`stable_id`,`version`)
) ENGINE=MyISAM AUTO_INCREMENT=21747 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
CREATE TABLE `translation_attrib` (
`translation_id` int(10) unsigned NOT NULL DEFAULT '0',
......@@ -868,7 +868,7 @@ CREATE TABLE `unmapped_reason` (
`summary_description` varchar(255) DEFAULT NULL,
`full_description` varchar(255) DEFAULT NULL,
PRIMARY KEY (`unmapped_reason_id`)
) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1;
CREATE TABLE `xref` (
`xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......
......@@ -24,6 +24,7 @@
175 \N patch patch_77_78_b.sql|source_column_increase
176 \N patch patch_77_78_c.sql|Change unmapped_reason_id from smallint to int
177 \N patch patch_78_79_a.sql|schema_version
178 \N patch patch_78_79_b.sql|bamcov support
1 \N schema_type core
2 \N schema_version 79
8 1 assembly.accession GCA_000292705.1
......
......@@ -126,7 +126,7 @@ CREATE TABLE `data_file` (
`version_lock` tinyint(1) NOT NULL DEFAULT '0',
`absolute` tinyint(1) NOT NULL DEFAULT '0',
`url` text,
`file_type` enum('BAM','BIGBED','BIGWIG','VCF') DEFAULT NULL,
`file_type` enum('BAM','BAMCOV','BIGBED','BIGWIG','VCF') DEFAULT NULL,
PRIMARY KEY (`data_file_id`),
UNIQUE KEY `df_unq_idx` (`coord_system_id`,`analysis_id`,`name`,`file_type`),
KEY `df_name_idx` (`name`),
......@@ -469,7 +469,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=InnoDB AUTO_INCREMENT=178 DEFAULT CHARSET=latin1;
) ENGINE=InnoDB AUTO_INCREMENT=179 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......
......@@ -169,7 +169,7 @@ CREATE TABLE data_file (
version_lock TINYINT(1) DEFAULT 0 NOT NULL,
absolute TINYINT(1) DEFAULT 0 NOT NULL,
url TEXT,
file_type ENUM('BAM','BIGBED','BIGWIG','VCF'),
file_type ENUM('BAM','BAMCOV','BIGBED','BIGWIG','VCF'),
PRIMARY KEY (data_file_id),
UNIQUE KEY df_unq_idx(coord_system_id, analysis_id, name, file_type),
......
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