Commit 9856de0a authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 3.2.0

parent 65c61e44

CMakeLists.txt

+1 −1
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@@ -2,7 +2,7 @@ cmake_minimum_required( VERSION 2.8.2 ) 


project( FLEXBAR )



set( SEQAN_APP_VERSION "3.1.0" )

set( SEQAN_APP_VERSION "3.2.0" )



include_directories( ${FLEXBAR_SOURCE_DIR}/include )

# link_directories( ${FLEXBAR_SOURCE_DIR}/lib )

README.md

+6 −6
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@@ -28,20 +28,20 @@ Flexbar source code as well as binaries for Linux and Mac OS can be downloaded o 
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 2.2.0 [here](https://github.com/seqan/seqan/releases/download/seqan-v2.2.0/seqan-library-2.2.0.tar.xz)

* Download Flexbar 3.1 source code [release](https://github.com/seqan/flexbar/releases)

* Download Flexbar 3.2 source code [release](https://github.com/seqan/flexbar/releases)



Decompress both files:



	tar xzf flexbar-3.1.0.tar.gz

	tar xzf flexbar-3.2.0.tar.gz

	tar xJf seqan-library-2.2.0.tar.xz



Move SeqAn include folder to Flexbar:



	mv seqan-library-2.2.0/include flexbar-3.1.0

	mv seqan-library-2.2.0/include flexbar-3.2.0



Use these commands for building:



	cd flexbar-3.1.0

	cd flexbar-3.2.0

	cmake .

	make
@@ -77,9 +77,9 @@ In this example, reads that are barcoded on left side are demultiplexed by speci 


	flexbar -r reads.fq -t target -b brc.fa -be LTAIL -a adp.fa



The second example shows how to trim compressed reads based on their quality scores in illumina version 1.8 format. Afterwards, provided adapters are removed in right trim-end mode, only if the overlap of adapter and read has at least length five with at most 40% errors.

The second example shows how to trim compressed reads based on their quality scores in illumina version 1.8 format. Afterwards, provided adapters are removed in right trim-end mode, only if the overlap of adapter and read has at least length 5 with at most 20% errors.



	flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.4

	flexbar -r reads.fq.gz -q TAIL -qf i1.8 -a adp.fa -ao 5 -at 0.2



For further examples visit the [manual](https://github.com/seqan/flexbar/wiki) page.

src/Flexbar.cpp

+5 −3
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@@ -2,7 +2,9 @@ 
   

   Flexbar - flexible barcode and adapter removal

   

   Version 3.1.0

   Version 3.2.0

   

   BSD 3-Clause License

   

   uses SeqAn library release 2.2.0

   and TBB library 4.0 or later
@@ -27,8 +29,8 @@ int main(int argc, const char* argv[]){ 
	using namespace std;

	using namespace seqan;

	

	const string version = "3.1";

	const string date    = "April 2018";

	const string version = "3.2";

	const string date    = "May 2018";

	

	ArgumentParser parser("flexbar");

src/Flexbar.h

+8 −7
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@@ -98,17 +98,18 @@ void loadAdapters(Options &o, const bool secondSet, const bool useAdapterFile){ 
		}

	}

	else{

		if(o.rcMode == RCOFF || o.rcMode == RCON){

			TBar bar;

			bar.id  = "cmdline";

			bar.seq = o.adapterSeq;

			o.adapters.push_back(bar);

		

		if(o.revCompAdapter){

		}

		if(o.rcMode == RCON || o.rcMode == RCONLY){

			TSeqStr adapterSeqRC = o.adapterSeq;

			seqan::reverseComplement(adapterSeqRC);

			

			TBar barRC;

			barRC.id  = "cmdline revcomp";

			barRC.id  = "cmdline_rc";

			barRC.seq = adapterSeqRC;

			o.adapters.push_back(barRC);

		}

src/FlexbarTypes.h

+27 −9
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@@ -11,17 +11,21 @@ class SeqRead { 
	TSeqStr seq;

	TString id, qual, umi;

	

	bool rmAdapter, rmAdapterRC;

	

	SeqRead(TSeqStr& sequence, TString& seqID) :

		seq(sequence),

		id(seqID),

		umi(""){

		rmAdapter(false),

		rmAdapterRC(false){

	}

	

	SeqRead(TSeqStr& sequence, TString& seqID, TString& quality) :

		seq(sequence),

		id(seqID),

		qual(quality),

		umi(""){

		rmAdapter(false),

		rmAdapterRC(false){

	}

};
@@ -60,7 +64,7 @@ struct AlignResults{ 
	int overlapLength, queryLength, tailLength;

	

	float allowedErrors;

	TSeqStr randTag;

	TSeqStr umiTag;

	std::string alString;

	

	AlignResults(){}
@@ -116,16 +120,30 @@ namespace flexbar{ 
		

		FString id;

		FSeqStr seq;

		bool rcAdapter;

		

		tbb::atomic<unsigned long> rmOverlap, rmFull;

		

		TBar() :

			rmOverlap(0),

			rmFull(0){

			rmFull(0),

			rcAdapter(false){

	    }

	};

	

	

	enum RevCompMode {

		RCOFF,

		RCON,

		RCONLY

	};

	

	enum AlignmentMode {

		ALIGNALL,

		ALIGNRCOFF,

		ALIGNRC

	};

	

	enum ComputeCycle {

		PRELOAD,

		COMPUTE,