NAME

CLIPSeqTools::CompareApp::all - Run all clipseqtools-compare analyses.

SYNOPSIS

clipseqtools-compare all [options/parameters]

DESCRIPTION

Run all clipseqtools-compare analyses.

Takes two libraries (one called input and one called reference) on which all single clipseqtools analyses have ran. Assumes that all single clipseqtools analyses used a common o_prefix for each library.

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
  --res_prefix <Str>      results prefix of clipseqtools analysis.
                          Should match the o_prefix used when running
                          clipseqtools on the library.

Input options for reference library.
  --r_driver <Str>        driver for database connection (eg. mysql,
                          SQLite).
  --r_database <Str>      database name or path to database file for
                          file based databases (eg. SQLite).
  --r_table <Str>         database table.
  --r_host <Str>          hostname for database connection.
  --r_user <Str>          username for database connection.
  --r_password <Str>      password for database connection.
  --r_records_class <Str> type of records stored in database.
  --r_filter <Filter>     same as filter but for reference library.
  --r_res_prefix <Str>    results prefix of clipseqtools analysis.
                          Should match the o_prefix used when running
                          clipseqtools on the reference library.

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_prefix <Str>        output path prefix. Script will create and add
                          extension to path. Default: ./

Other options.
  -v --verbose           print progress lines and extra information.
  -h -? --usage --help   print help message