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

       Faidx -- Perl extension for accessing bgzip compressed and indexed FASTA using htslib

SYNOPSIS

        #include the module
        use Bio::DB::HTS::Faidx;

        #create the index object
        my $fasta = "$Bin/data/Saccharomyces_cerevisiae.R64-1-1.dna.chromosome.I.fa.gz" ;
        my $location = "I:1-100" ;
        my $seq_id = "I" ;
        my $index = Bio::DB::HTS::Faidx->new($fasta);

        #get sequence using the location
        my $seq = "" ;
        my $length = 0 ;
        ($seq, $length) = $index->get_sequence($location);

        $seq = $index->get_sequence_no_length($location);
        $length = $index->length($seq_id);

        #get sequence using the separate parameters.
        #Note here that the sequence start and end points are zero indexed, so code accordingly.
        ($seq, $length) = $index->get_sequence2("I",1,99);
        $seq = $index->get_sequence2_no_length("I",1,99);

        my @seq_ids = $index->get_all_sequence_ids();

        #returns 1 if sequence ID is present, 0 if not
        my $has_seq = $index->has_sequence('I');

AUTHOR

       Rishi Nag