NAME
Bio::Cigar - Parse CIGAR strings and translate coordinates to/from
reference/query
SYNOPSIS
use 5.014;
use Bio::Cigar;
my $cigar = Bio::Cigar->new("2M1D1M1I4M");
say "Query length is ", $cigar->query_length;
say "Reference length is ", $cigar->reference_length;
my ($qpos, $op) = $cigar->rpos_to_qpos(3);
say "Alignment operation at reference position 3 is $op";
DESCRIPTION
Bio::Cigar is a small library to parse CIGAR strings ("Compact
Idiosyncratic Gapped Alignment Report"), such as those used in the SAM
file format. CIGAR strings are a run-length encoding which minimally
describes the alignment of a query sequence to an (often longer)
reference sequence.
Parsing follows the SAM v1 spec
<
http://samtools.github.io/hts-specs/SAMv1.pdf> for the "CIGAR" column.
Parsed strings are represented by an object that provides a few utility
methods.
ATTRIBUTES
All attributes are read-only.
string
The CIGAR string for this object.
reference_length
The length of the reference sequence segment aligned with the query
sequence described by the CIGAR string.
query_length
The length of the query sequence described by the CIGAR string.
ops
An arrayref of "[length, operation]" tuples describing the CIGAR string.
Lengths are integers, possible operations are below.
CIGAR operations
The CIGAR operations are given in the following table, taken from the
SAM v1 spec:
Op Description
‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾
M alignment match (can be a sequence match or mismatch)
I insertion to the reference
D deletion from the reference
N skipped region from the reference
S soft clipping (clipped sequences present in SEQ)
H hard clipping (clipped sequences NOT present in SEQ)
P padding (silent deletion from padded reference)
= sequence match
X sequence mismatch
• H can only be present as the first and/or last operation.
• S may only have H operations between them and the ends of the string.
• For mRNA-to-genome alignment, an N operation represents an intron.
For other types of alignments, the interpretation of N is not defined.
• Sum of the lengths of the M/I/S/=/X operations shall equal the length of SEQ.
CONSTRUCTOR
new
Takes a CIGAR string as the sole argument and returns a new Bio::Cigar
object.
METHODS
rpos_to_qpos
Takes a reference position (origin 1, base-numbered) and returns the
corresponding position (origin 1, base-numbered) on the query sequence.
Indels affect how the numbering maps from reference to query.
In list context returns a tuple of "[query position, operation at
position]". Operation is a single-character string. See the table of
CIGAR operations.
If the reference position does not map to the query sequence (as with a
deletion, for example), returns "undef" or "[undef, operation]".
qpos_to_rpos
Takes a query position (origin 1, base-numbered) and returns the
corresponding position (origin 1, base-numbered) on the reference
sequence. Indels affect how the numbering maps from query to reference.
In list context returns a tuple of "[references position, operation at
position]". Operation is a single-character string. See the table of
CIGAR operations.
If the query position does not map to the reference sequence (as with an
insertion, for example), returns "undef" or "[undef, operation]".
op_at_rpos
Takes a reference position and returns the operation at that position.
Simply a shortcut for calling "rpos_to_qpos" in list context and
discarding the first return value.
op_at_qpos
Takes a query position and returns the operation at that position.
Simply a shortcut for calling "qpos_to_rpos" in list context and
discarding the first return value.
AUTHOR
Thomas Sibley <
[email protected]>
COPYRIGHT
Copyright 2014- Mullins Lab, Department of Microbiology, University of
Washington.
LICENSE
This library is free software; you can redistribute it and/or modify it
under the GNU General Public License, version 2.
SEE ALSO
SAMv1 spec <
http://samtools.github.io/hts-specs/SAMv1.pdf>
