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.IX Title "Bio::DB::HTS::Constants 3pm"
.TH Bio::DB::HTS::Constants 3pm 2024-03-07 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH LICENSE
.IX Header "LICENSE"
Copyright [2015\-2018] EMBL-European Bioinformatics Institute
.PP
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
.PP
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\&     http://www.apache.org/licenses/LICENSE\-2.0
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.PP
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.
.SH NAME
Bio::DB::HTS::Constants \-\- Constants for use with SAM/BAM
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\& use Bio::DB::HTS::Constants;
\& my $pad_flag = BAM_CPAD;
.Ve
.SH DESCRIPTION
.IX Header "DESCRIPTION"
This module exports several constants for use with the SAM/BAM
module. See the SAM documentation for their interpretation.
.IP "Cigar operations" 4
.IX Item "Cigar operations"
.Vb 9
\&  BAM_CIGAR_SHIFT
\&  BAM_CIGAR_MASK
\&  BAM_CMATCH
\&  BAM_CINS
\&  BAM_CDEL
\&  BAM_CREF_SKIP
\&  BAM_CSOFT_CLIP
\&  BAM_CHARD_CLIP
\&  BAM_CPAD
.Ve
.IP FLAGS 4
.IX Item "FLAGS"
A hashref that maps flag values to human-readable names. For example:
.Sp
.Vb 1
\& FLAGS\->{0x0008} == \*(AqM_UNMAPPED\*(Aq
.Ve
.IP RFLAGS 4
.IX Item "RFLAGS"
The reverse of FLAGS:
.Sp
.Vb 1
\& RFLAGS\->{M_UNMAPPED} == 0x0008
.Ve
.SH AUTHOR
.IX Header "AUTHOR"
Rishi Nag <rishi@ebi.ac.uk<gt>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Perl, Bio::DB::HTS, Bio::DB::Bam::Alignment