Provided by: libbio-db-hts-perl_3.01-3build2_amd64 bug

LICENSE

       Copyright [2015-2018] EMBL-European Bioinformatics Institute

       Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
       except in compliance with the License.  You may obtain a copy of the License at

            http://www.apache.org/licenses/LICENSE-2.0

       Unless required by applicable law or agreed to in writing, software distributed under the
       License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
       either express or implied.  See the License for the specific language governing
       permissions and limitations under the License.

NAME

       Bio::DB::HTS::AlignWrapper -- Add high-level methods to Bio::DB::HTS::Alignment

SYNOPSIS

       See Bio::DB::HTS::Alignment.

DESCRIPTION

       This is a wrapper around Bio::DB::HTS::Alignment that adds the following high-level
       methods. These are described in detail in "High-level Bio::DB::HTS::Alignment methods" in
       Bio::DB::HTS::Alignment.

        add_segment()         add a new subfeature to split alignments
        get_SeqFeatures()     fetch subfeatures from split alignments
        split_splices()       process cigar strings to produce split alignments
        expand_flags()        return true if flags should be expanded into tags
        seq_id()              return human-readable reference sequence name
        seq()                 return Bio::PrimarySeq object for reference sequence
        subseq()              return a subsequence across the indicated range
        mate_seq_id()         return human-readable mate reference sequence name
        dna()                 return the DNA of the reference sequence
        tam_line()            return the text representation of the alignment
        attributes()          synonym for get_tag_values()
        get_all_tags()        return all tag names
        get_tag_values()      return the values of the given tag
        has_tag()             return true if the given tag is defined

SEE ALSO

       Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Constants

AUTHOR

       Rishi Nag <rishi@ebi.ac.uk<gt>