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CLIPSeqTools-0.1.3
River stage zero No dependents
1 ++
/ CLIPSeqTools::PreprocessApp::sam_to_sqlite

NAME

CLIPSeqTools::PreprocessApp::sam_to_sqlite - Load a SAM file in an SQLite database.

SYNOPSIS

clipseqtools-preprocess sam_to_sqlite [options/parameters]

DESCRIPTION

Store alignments from a SAM file into and SQLite database. If SAM tag XC:i exists it will be used as the copy number of the record.

OPTIONS

  Input options.
    --sam_file <Str>       sam file to be stored in database. If not
                           specified STDIN is used.
    --records_class <Str>  type of records stored in SAM file. [Default:
                           GenOOx::Data::File::SAMstar::Record]

  Database options.
    --database <Str>       database name or path. Will be created.
    --table <Str>          database table. Will be created.
    --drop <Str>           drop table if it already exists.

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