NAME

CLIPSeqTools::PreprocessApp::annotate_with_file - Annotate alignments in a database table with regions from a BED/SAM file.

SYNOPSIS

clipseqtools-preprocess annotate_with_file [options/parameters]

DESCRIPTION

Annotate alignments in a database table with regions from a BED/SAM file. Adds a user defined column that will be NOT NULL if an alignment is contained within a region from the file and NULL otherwise.

OPTIONS

Input options for library.
  --driver <Str>         driver for database connection (eg. mysql,
                         SQLite).
  --database <Str>       database name or path to database file for file
                         based databases (eg. SQLite).
  --table <Str>          database table.
  --host <Str>           hostname for database connection.
  --user <Str>           username for database connection.
  --password <Str>       password for database connection.
  --records_class <Str>  type of records stored in database.
  --filter <Filter>      filter library. May be used multiple times.
                         Syntax: column_name="pattern"
                         e.g. keep reads with deletions AND not repeat
                              masked AND longer than 31
                              --filter deletion="def" 
                              --filter rmsk="undef" .
                              --filter query_length=">31".
                         Operators: >, >=, <, <=, =, !=, def, undef

Other input
  --a_type <Str>         type of file with annotation regions (i.e. BED,
                         SAM).
  --a_file <Str>         file with annotation regions.

Database options.
  --drop                 drop column if it already exists (not
                         supported in SQlite).

Other options.
  --column <Str>         name for the new annotation column.
  --both_strands         annotate both strands irrespective of the
                         region strand specified in the file. May be
                         useful for repeats where only one strand is
                         usually provided.
  -v --verbose           print progress lines and extra information.
  -h -? --usage --help   print help message