|Bio::DB::HTS::Query(3pm)||User Contributed Perl Documentation||Bio::DB::HTS::Query(3pm)|
Copyright [2015-2018] EMBL-European Bioinformatics Institute
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Rishi Nag <firstname.lastname@example.org<gt>
Bio::DB::HTS::Query -- Object representing the query portion of a BAM/SAM alignment
Given an alignment retrieved from a Bio::DB::HTS database,
my $query = $alignment->query; my $name = $query->display_name; my $start = $query->start; my $end = $query->end; my $dna = $query->dna; # dna string my $seq = $query->seq; # Bio::PrimarySeq object my @scores = $query->qscore; # quality score
This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment.
- $seqid = $query->seq_id
- The name of the read.
- $name = $query->name
- The read name (same as seq_id in this case).
- $name = $query->display_name
- The read display_name (same as seq_id in this case).
- $tag = $query->primary_tag
- The string "match".
- $tag = $query->source_tag
- The string "sam/bam".
- $start = $query->start
- The start of the match in read coordinates.
- $end = $query->end
- The end of the match in read coordinates;
- $len = $query->length
- The length of the read.
- $seq = $query->seq
- A Bio::PrimarySeq representing the read sequence in REFERENCE orientation.
- $scores = $query->qscore
- The read quality scores. In a list context, a list of integers equal in length to the read sequence length. In a scalar context, an array ref. The qscores are in REFERENCE sequence orientation.
- $dna = $query->dna
- The DNA string in reference sequence orientation.
- $strand = $query->strand
- If the query was reversed to align it, -1. Otherwise +1.
- $seq = $query->subseq($start,$end)
- Return a Bio::PrimarySeq object representing the requested subsequence on the read.
Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants