NAME

libraries_relative_read_density.pl

SYNOPSIS

libraries_relative_read_density.pl [options/parameters]

For a library A and a reference library B, measure the density of A reads around the middle position of B reads.

Input options for primary library.
    -p_type <Str>          input type (eg. DBIC, BED).
    -p_file <Str>          input file. Only works if p_type specifies a file type.
    -p_driver <Str>        driver for database connection (eg. mysql, SQLite). Only works if p_type is DBIC.
    -p_database <Str>      database name or path to database file for file based databases (eg. SQLite). Only works if p_type is DBIC.
    -p_table <Str>         database table. Only works if p_type is DBIC.
    -p_host <Str>          hostname for database connection. Only works if p_type is DBIC.
    -p_user <Str>          username for database connection. Only works if p_type is DBIC.
    -p_password <Str>      password for database connection. Only works if p_type is DBIC.
    -p_records_class <Str> type of records stored in database (Default: GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3).

Input options for reference library.
    -r_type <Str>          input type (eg. DBIC, BED).
    -r_file <Str>          input file. Only works if r_type specifies a file type.
    -r_driver <Str>        driver for database connection (eg. mysql, SQLite). Only works if r_type is DBIC.
    -r_database <Str>      database name or path to database file for file based databases (eg. SQLite). Only works if r_type is DBIC.
    -r_table <Str>         database table. Only works if r_type is DBIC.
    -r_host <Str>          hostname for database connection. Only works if r_type is DBIC.
    -r_user <Str>          username for database connection. Only works if r_type is DBIC.
    -r_password <Str>      password for database connection. Only works if r_type is DBIC.
    -r_records_class <Str> type of records stored in database (Default: GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3).

Other input.
    -rname_sizes <Str>     file with sizes for reference alignment sequences (rnames). Must be tab delimited (chromosome\tsize) with one line per rname

Output.
    -o_file <Str>          filename for output file. If path does not exist it will be created.

Input Filters (only for DBIC input type).
    -p_filter <Filter>     filter primary collection. Option can be given multiple times. 
    -r_filter <Filter>     filter reference collection. Option can be given multiple times.
                           Syntax: column_name="pattern"
                             e.g. -p_filter deletion="def" -p_filter rmsk="undef" to keep only reads with deletions and not repeat masked.
                             e.g. -r_filter query_length=">31" -r_filter query_length="<=50" to keep reads longer than 31 and shorter or equal to 50.
                           Supported operators: ">", ">=", "<", "<=", "=", "!=","def", "undef"

Other options.
    -span <Int>            the region around reference records in which density is measured
    -v                     verbosity. If used progress lines are printed.
    -h                     print help message
    -man                   show man page

DESCRIPTION

For two libraries, a primary and a reference one, measure the density of primary reads around the middle position of the reference ones.