New upstream version 3.5.0

project( FLEXBAR )

set( SEQAN_APP_VERSION "3.4.0" )

set( SEQAN_APP_VERSION "3.5.0" )

include_directories( ${FLEXBAR_SOURCE_DIR}/include )

# link_directories( ${FLEXBAR_SOURCE_DIR}/lib )

## Flexbar – flexible barcode and adapter removal

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fasta and fastq format, e.g. from the Illumina platform.

The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Several adapter removal presets for Illumina libraries are included. Flexbar computes exact overlap alignments using SIMD and multicore parallelism. Moreover, trimming and filtering features are provided, e.g. trimming of homopolymers at read ends. Flexbar increases read mapping rates and improves genome as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The software supports data in fasta and fastq format from multiple sequencing platforms.

Refer to the [manual](https://github.com/seqan/flexbar/wiki) or contact [Johannes Roehr](https://github.com/jtroehr) for support with this application.

### Download

Flexbar source code as well as binaries for Linux and Mac OS can be downloaded on the [release](https://github.com/seqan/flexbar/releases) page. Please follow instructions for building or setup of binaries below. Additionally, Flexbar is available via package manager on Debian systems and in Conda. Versions before 2.4 can be found on the [old](https://sourceforge.net/projects/flexbar) page.

Flexbar source code as well as binaries for Linux and Mac OS can be downloaded on the [release](https://github.com/seqan/flexbar/releases) page. Please follow instructions for building or setup of binaries below. Additionally, Flexbar is available via package manager on Debian systems, in Homebrew, and in Bioconda. Versions before 2.4 can be found on the [old](https://sourceforge.net/projects/flexbar) page.

Installation with package managers:

* Debian: `sudo apt install flexbar`

* Homebrew: `brew install brewsci/science/flexbar`

* Bioconda: `conda install -c bioconda flexbar`

To get the latest version and best performance consider to build Flexbar from source.

### Building from source

Make sure that `cmake` is available, as well as development and runtime files of the TBB library 4.0 or later (Intel Threading Building Blocks). For example on Debian systems, install the packages `libtbb-dev` and `libtbb2`. Furthermore, the SeqAn library and a compiler that supports C++14 is required:

* Get SeqAn library version 2.4.0 [here](https://github.com/seqan/seqan/releases/download/seqan-v2.4.0/seqan-library-2.4.0.tar.xz)

* Download Flexbar 3.4 source code [release](https://github.com/seqan/flexbar/releases)

* Download Flexbar 3.5.0 source code [release](https://github.com/seqan/flexbar/releases)

Decompress both files:

	tar xzf flexbar-3.4.0.tar.gz

	tar xzf flexbar-3.5.0.tar.gz

	tar xJf seqan-library-2.4.0.tar.xz

Move SeqAn include folder to Flexbar:

	mv seqan-library-2.4.0/include flexbar-3.4.0

	mv seqan-library-2.4.0/include flexbar-3.5.0

Use these commands for building:

	cd flexbar-3.4.0

	cd flexbar-3.5.0

	cmake .

	make

#### Linux

Adjust lib search path to include the absolute path of the Flexbar directory containing the lib file libtbb.so.2 for the current terminal session, or permanently in shell startup scripts:

	export LD_LIBRARY_PATH=/path/FlexbarDir:$LD_LIBRARY_PATH

	export LD_LIBRARY_PATH=/YourPath/flexbar-3.5.0-linux:$LD_LIBRARY_PATH

#### Mac OS

It applies the same as for Linux. Make the file libtbb.dylib available by setting the lib search path:

	export DYLD_LIBRARY_PATH=/path/FlexbarDir:$DYLD_LIBRARY_PATH

	export DYLD_LIBRARY_PATH=/YourPath/flexbar-3.5.0-macos:$DYLD_LIBRARY_PATH

### Program usage

For paired-end libraries, specify both files with paired reads and a fasta file with adapters for removal. Given adapters are trimmed in right mode per default. It is recommended to activate the pair overlap detection in case of standard paired reads. This increases the sensitivity by removing very short parts of adapters if an overlap is detected for a pair.

	flexbar -r r1.fq -p r2.fq -a adapters.fa -ap ON

	flexbar -r r1.fq -p r2.fq -a a1.fa -a2 a2.fa -ap ON

#### Adapter removal presets

#!/usr/bin/env perl

# Flexbar wrapper for Galaxy tool definition, version 3.5.0

# Author: Johannes Roehr

use warnings;

use strict;

my $format;

my @inFiles;

my @outFiles;

my $compression = "";

foreach(0..$#ARGV){

	my $arg = $ARGV[$_];

	if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){

		if(defined $format && $format ne $1){

			warn "Read files should have the same format.\n";

			exit 1;

		}

		$format = $1;

		my $file = $arg;

		$arg =~ s/\.fastq\w+$/\.fastq/;

		$arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;

		$arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;

		$compression = "GZ"  if $arg =~ /\.fastq\.gz$/;

		$compression = "BZ2" if $arg =~ /\.fastq\.bz2$/;

		$ARGV[$_] = $arg;

		if($arg =~ /\.dat_input\w\.fastq$/ || $arg =~ /\.dat_input\w\.fastq\.gz$/ || $arg =~ /\.dat_input\w\.fastq\.bz2$/){

			push @inFiles, $arg;

			rename $file, $arg;

		}

		push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;

	}

}

my $barcoded = 0;

$barcoded = 1 if $ARGV[$#ARGV] =~ /barcoded$/;

my $call = join " ", @ARGV[0..($#ARGV - $barcoded)];

# $call = $call ." --zip-output ". $compression if $barcoded && $compression ne "";

system $call and exit 1;

unlink $_ or warn "Could not unlink $_: $!" foreach(@inFiles);

if($barcoded){

	$format =~ s/\.gz//;

	$format =~ s/\.bz2//;

	foreach(<$ARGV[$#ARGV]/flexbarOut*.fastq*>){

		my $file = $_;

		s/fastq$/$format/;

		# s/fastq\.gz$/$format/;

		# s/fastq\.bz2$/$format/;

		rename $file, $_;

	}

}

else{

	foreach(@outFiles){

		my $file = $_;

		s/\.fastq$//;

		s/\.fastq\.gz$//;

		s/\.fastq\.bz2$//;

		rename $file, $_;

	}

}

   Flexbar - flexible barcode and adapter removal

   Version 3.4.0

   Version 3.5.0

   BSD 3-Clause License

	using namespace std;

	using namespace seqan;

	const string version = "3.4.0";

	const string date    = "June 2018";

	const string version = "3.5.0";

	const string date    = "May 2019";

	ArgumentParser parser("flexbar");