ExtractRegex #

Extract a regexp result. Stores an empty string if not found.

[[step]]
    action = "ExtractRegex"
    out_label = "mytag"
    search = "^CT(..)CT"
    replacement = "$1"  # optional. standard regex replacement syntax
    source = "read1" # An input segment (to read from sequence), 
                     # a name:<segment> to read from a read's name or
                    # a tag:tag_label to read from an existing tag..

This transformation searches for a regular expression pattern in the specified read and extracts the matching portion as a tag.

The value actually ’extracted’ is after replacement has been performed.

See the regex documentation for details on the syntax supported.

Note that you need to ‘double up’ on backslashes for character classes inside the search string.

The replacement supports replacing other tag’s values into your string. Use [[tag]] to achieve that.

Extracting from names or tags yields string tags, extracting from the sequence yields Location tags.

The quality of these extracted tags is always ‘I’.