.\" -*- mode: troff; coding: utf-8 -*-
.\" Automatically generated by Pod::Man 5.01 (Pod::Simple 3.43)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" \*(C` and \*(C' are quotes in nroff, nothing in troff, for use with C<>.
.ie n \{\
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.nr rF 0
.if \n(.g .if rF .nr rF 1
.if (\n(rF:(\n(.g==0)) \{\
.    if \nF \{\
.        de IX
.        tm Index:\\$1\t\\n%\t"\\$2"
..
.        if !\nF==2 \{\
.            nr % 0
.            nr F 2
.        \}
.    \}
.\}
.rr rF
.\" ========================================================================
.\"
.IX Title "Bio::DB::HTS::Kseq 3pm"
.TH Bio::DB::HTS::Kseq 3pm 2024-03-07 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.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
.Vb 1
\&     http://www.apache.org/licenses/LICENSE\-2.0
.Ve
.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::Kseq \- Bindings to Kseq
.SH DESCRIPTION
.IX Header "DESCRIPTION"
Bindings to the Kseq library for iterating through a locally held FASTA/FASTQ file very quickly. Supports compressed and uncompressed files alongside filehandles.
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 8
\&  my $kseq = Bio::DB::HTS::Kseq\->new(\*(Aqpath/to/file\*(Aq);
\&  my $iter = $kseq\->iterator();
\&  while(my $r = $iter\->next_seq()) {
\&    say $r\->name;
\&    say $r\->desc;
\&    say $r\->seq;
\&    say $r\->qual;
\&  }
\&
\&  # Allowing the object to go out of scope will close down all file handles
.Ve
.SS METHODS
.IX Subsection "METHODS"
.ie n .IP """new""" 8
.el .IP \f(CWnew\fR 8
.IX Item "new"
.Vb 1
\&  my $kseq = Bio::DB::HTS::Kseq\->new(\*(Aqpath/to/file\*(Aq);
.Ve
.Sp
Returns an instance of this object from a file path.
.ie n .IP """newfh""" 8
.el .IP \f(CWnewfh\fR 8
.IX Item "newfh"
.Vb 3
\&  open my $fh, \*(Aq<\*(Aq, \*(Aqpath\*(Aq or die "Cannot open path: $!";
\&  binmode $fh;
\&  my $kseq = Bio::DB::HTS::Kseq\->newfh($fh);
.Ve
.Sp
Returns an instance of this object from an opened file handle. This supports any known Perl glob/filehandle type
.ie n .IP """iterator""" 8
.el .IP \f(CWiterator\fR 8
.IX Item "iterator"
.Vb 1
\&  my $iter = $kseq\->iterator();
.Ve
.Sp
Returns the kseq iterator object