oracular (3) Bio::DB::HTS::AlignWrapper.3pm.gz
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>