tabix(1) [debian man page]
tabix(1) Bioinformatics tools tabix(1) NAME
bgzip - Block compression/decompression utility tabix - Generic indexer for TAB-delimited genome position files SYNOPSIS
bgzip [-cdhB] [-b virtualOffset] [-s size] [file] tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol] [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]] DESCRIPTION
Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the com- mand-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. OPTIONS OF TABIX
-p STR Input format for indexing. Valid values are: gff, bed, sam, vcf and psltab. This option should not be applied together with any of -s, -b, -e, -c and -0; it is not used for data retrieval because this setting is stored in the index file. [gff] -s INT Column of sequence name. Option -s, -b, -e, -S, -c and -0 are all stored in the index file and thus not used in data retrieval. [1] -b INT Column of start chromosomal position. [4] -e INT Column of end chromosomal position. The end column can be the same as the start column. [5] -S INT Skip first INT lines in the data file. [0] -c CHAR Skip lines started with character CHAR. [#] -0 Specify that the position in the data file is 0-based (e.g. UCSC files) rather than 1-based. -h Print the header/meta lines. -B The second argument is a BED file. When this option is in use, the input file may not be sorted or indexed. The entire input will be read sequentially. Nonetheless, with this option, the format of the input must be specificed correctly on the command line. -f Force to overwrite the index file if it is present. -l List the sequence names stored in the index file. EXAMPLE
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz; tabix -p gff sorted.gff.gz; tabix sorted.gff.gz chr1:10,000,000-20,000,000; NOTES
It is straightforward to achieve overlap queries using the standard B-tree index (with or without binning) implemented in all SQL data- bases, or the R-tree index in PostgreSQL and Oracle. But there are still many reasons to use tabix. Firstly, tabix directly works with a lot of widely used TAB-delimited formats such as GFF/GTF and BED. We do not need to design database schema or specialized binary formats. Data do not need to be duplicated in different formats, either. Secondly, tabix works on compressed data files while most SQL databases do not. The GenCode annotation GTF can be compressed down to 4%. Thirdly, tabix is fast. The same indexing algorithm is known to work effi- ciently for an alignment with a few billion short reads. SQL databases probably cannot easily handle data at this scale. Last but not the least, tabix supports remote data retrieval. One can put the data file and the index at an FTP or HTTP server, and other users or even web services will be able to get a slice without downloading the entire file. AUTHOR
Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching. SEE ALSO
samtools(1) tabix-0.2.0 11 May 2010 tabix(1)
Check Out this Related Man Page
DB2_STATISTICS(3) 1 DB2_STATISTICS(3) db2_statistics - Returns a result set listing the index and statistics for a table SYNOPSIS
resource db2_statistics (resource $connection, string $qualifier, string $schema, string $table-name, bool $unique) DESCRIPTION
Returns a result set listing the index and statistics for a table. PARAMETERS
o $connection - A valid connection to an IBM DB2, Cloudscape, or Apache Derby database. o $qualifier - A qualifier for DB2 databases running on OS/390 or z/OS servers. For other databases, pass NULL or an empty string. o $schema - The schema that contains the targeted table. If this parameter is NULL, the statistics and indexes are returned for the schema of the current user. o $table_name - The name of the table. o $unique - An integer value representing the type of index information to return. o $0 - Return only the information for unique indexes on the table. o $1 - Return the information for all indexes on the table. RETURN VALUES
Returns a statement resource with a result set containing rows describing the statistics and indexes for the base tables matching the specified parameters. The rows are composed of the following columns: +--------------+---------------------------------------------------+ | Column name | | | | | | | Description | | | | +--------------+---------------------------------------------------+ | TABLE_CAT | | | | | | | The catalog that contains the table. The value is | | | NULL if this table does not have catalogs. | | | | | TABLE_SCHEM | | | | | | | Name of the schema that contains the table. | | | | | TABLE_NAME | | | | | | | Name of the table. | | | | | NON_UNIQUE | | | | | | | An integer value representing whether the index | | | prohibits unique values, or whether the row rep- | | | resents statistics on the table itself: | | | | | | box, tab (|); c | c | . T{ Return value | | | | | | Parameter type | | | | +--------------+---------------------------------------------------+ |0 (SQL_FALSE) | | | | | | | The index allows duplicate values. | | | | |1 (SQL_TRUE) | | | | | | | The index values must be unique. | | | | | | | | NULL | | | | | | | This row is statistics information for the table | | | itself. | | | | +--------------+---------------------------------------------------+ T} T{ INDEX_QUALIFIER T} |T{ A string value representing the qualifier that would have to be prepended to INDEX_NAME to fully qualify the index. T} T{ INDEX_NAME T} |T{ A string representing the name of the index. T} T{ TYPE T} |T{ An integer value representing the type of information contained in this row of the result set: +------------------------+---------------------------------------------------+ | Return value | | | | | | | Parameter type | | | | +------------------------+---------------------------------------------------+ | 0 (SQL_TABLE_STAT) | | | | | | | The row contains statistics about the table | | | itself. | | | | |1 (SQL_INDEX_CLUSTERED) | | | | | | | The row contains information about a clustered | | | index. | | | | | 2 (SQL_INDEX_HASH) | | | | | | | The row contains information about a hashed | | | index. | | | | | 3 (SQL_INDEX_OTHER) | | | | | | | The row contains information about a type of | | | index that is neither clustered nor hashed. | | | | +------------------------+---------------------------------------------------+ T} T{ ORDINAL_POSITION T} |T{ The 1-indexed position of the column in the index. NULL if the row contains statistics information about the table itself. T} T{ COLUMN_NAME T} |T{ The name of the column in the index. NULL if the row contains statistics information about the table itself. T} T{ ASC_OR_DESC T} |T{ A if the column is sorted in ascending order, D if the column is sorted in descending order, NULL if the row contains statistics informa- tion about the table itself. T} T{ CARDINALITY T} |T{ If the row contains information about an index, this column contains an integer value representing the number of unique values in the index. If the row contains information about the table itself, this column contains an integer value representing the number of rows in the table. T} T{ PAGES T} |T{ If the row contains information about an index, this column contains an integer value representing the number of pages used to store the index. If the row contains information about the table itself, this column contains an integer value representing the number of pages used to store the table. T} T{ FILTER_CONDITION T} |T{ Always returns NULL. T} SEE ALSO
db2_column_privileges(3), db2_columns(3), db2_foreign_keys(3), db2_primary_keys(3), db2_procedure_columns(3), db2_procedures(3), db2_spe- cial_columns(3), db2_table_privileges(3), db2_tables(3). PHP Documentation Group DB2_STATISTICS(3)