Commit 7418012d authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 1.0.10+ds

parent cd703265

.project

0 → 100644
+11 −0
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8"?>

<projectDescription>

	<name>Sniffles</name>

	<comment></comment>

	<projects>

	</projects>

	<buildSpec>

	</buildSpec>

	<natures>

	</natures>

</projectDescription>

CMakeLists.txt

+2 −2
Original line number Diff line number Diff line
@@ -7,9 +7,9 @@ option(STATIC "Build static binary" OFF) 
 set( SNIF_VERSION_MINOR 0 )

IF(CMAKE_BUILD_TYPE STREQUAL "Debug")

    message(STATUS "Building in debug mode!")

    set( SNIF_VERSION_BUILD 8-debug )

    set( SNIF_VERSION_BUILD 10-debug )

else()

	set( SNIF_VERSION_BUILD 8 )

	set( SNIF_VERSION_BUILD 10 )

ENDIF()

README.md

+20 −2
Original line number Diff line number Diff line
@@ -4,6 +4,24 @@ Sniffles is a structural variation caller using third generation sequencing (Pac 


Please see our github wiki for more information (https://github.com/fritzsedlazeck/Sniffles/wiki)





# How to build Sniffles

<pre>wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz

tar xzvf Sniffles.tar.gz

cd Sniffles-master/

mkdir -p build/

cd build/

cmake ..

make



cd ../bin/sniffles*

./sniffles</pre>



Note Mac users often have to provide parameters to the cmake command:

<pre>cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 .. 

</pre>





**************************************

## NGMLR

Sniffles performs best with the mappings of NGMLR our novel long read mapping method.
@@ -12,8 +30,8 @@ https://github.com/philres/ngmlr 


****************************************

## Citation:

Please see and cite our preprint:

http://www.biorxiv.org/content/early/2017/07/28/169557

Please see and cite our paper:

https://www.nature.com/articles/s41592-018-0001-7

  

**************************************

## Poster & Talks:

src/Alignment.cpp

+63 −54
Original line number Diff line number Diff line
@@ -136,6 +136,7 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de 
	if (al->CigarData[0].Type == 'S') {

		read_pos += al->CigarData[0].Length;

	}



	for (size_t i = 0; i < al->CigarData.size(); i++) {

		if (al->CigarData[i].Type == 'M') {

			pos += al->CigarData[i].Length;
@@ -176,15 +177,16 @@ vector<differences_str> Alignment::summarizeAlignment(std::vector<indel_str> &de 
		}

	}



	/*if (flag) {

	//exit(0);

	if (flag) {

		std::cout << "FIRST:" << std::endl;

		for (size_t i = 0; i < events.size(); i++) {

	 if (abs(events[i].type) > 200) {

			// if (abs(events[i].type) > 200) {

			cout << events[i].position << " " << events[i].type << endl;

	 }

			// }

		}

		cout << endl;

	 }*/

	}



//set ref length requ. later on:

	this->ref_len = pos - getPosition(); //TODO compare to get_length!
@@ -676,6 +678,7 @@ bool Alignment::overlapping_segments(vector<aln_str> entries) { 
	return (entries.size() == 2 && abs(entries[0].pos - entries[1].pos) < 100);

}

vector<aln_str> Alignment::getSA(RefVector ref) {



	string sa;

	vector<aln_str> entries;

	if (al->GetTag("SA", sa) && !sa.empty()) {
@@ -690,7 +693,7 @@ vector<aln_str> Alignment::getSA(RefVector ref) { 
		uint32_t sv;

		al->GetTag("SV", sv);

		tmp.cross_N = ((sv & Ns_CLIPPED));

		bool flag = strcmp(getName().c_str(), Parameter::Instance()->read_name.c_str()) == 0;

		bool flag = strcmp(getName().c_str(),"0bac61ef-7819-462b-ae3d-32c68fe580c0")==0; //Parameter::Instance()->read_name.c_str()) == 0;



		get_coords(tmp, tmp.read_pos_start, tmp.read_pos_stop);

		if (flag) {
@@ -791,8 +794,7 @@ vector<aln_str> Alignment::getSA(RefVector ref) { 
double Alignment::get_scrore_ratio() {

	uint score = -1;

	uint subscore = -1;

	if (al->GetTag("AS", score)) {

		al->GetTag("XS", subscore);

	if (al->GetTag("AS", score) && al->GetTag("XS", subscore)) {

		if (subscore == 0) {

			subscore = 1;

		}
@@ -804,6 +806,7 @@ bool Alignment::get_is_save() { 
	string sa;



	double score = get_scrore_ratio(); //TODO should I use this again for bwa?

//	cout<<score<<endl;



	return !((al->GetTag("XA", sa) && !sa.empty()) || (al->GetTag("XT", sa) && !sa.empty())) && (score == -1 || score > Parameter::Instance()->score_treshold); //|| //TODO: 7.5

}
@@ -923,6 +926,7 @@ std::string Alignment::get_md() { 
		return md;

	} else {

		std::cerr << "No MD string detected! Check bam file! Otherwise generate using e.g. samtools." << std::endl;

		cout<<"MD: TEST" << this->getName()<<endl;

		exit(0);

	}

	return md;
@@ -1056,6 +1060,8 @@ vector<int> Alignment::get_avg_diff(double & dist, double & avg_del, double & av 
//computeAlignment();

//cout<<alignment.first<<endl;

//cout<<alignment.second<<endl;

	avg_del = 0;

	avg_ins = 0;

	vector<int> mis_per_window;

	std::vector<indel_str> dels;

	vector<differences_str> event_aln = summarizeAlignment(dels);
@@ -1070,6 +1076,7 @@ vector<int> Alignment::get_avg_diff(double & dist, double & avg_del, double & av 
	double del = 0;

	double ins = 0;

	double mis = 0;

	if (event_aln.size() > 1) {

		double length = event_aln[event_aln.size() - 1].position - event_aln[0].position;

		for (size_t i = 0; i < event_aln.size(); i++) {

			if (i != 0) {
@@ -1092,12 +1099,14 @@ vector<int> Alignment::get_avg_diff(double & dist, double & avg_del, double & av 
				avg_ins += event_aln[i].type * -1;

			}

		}



		//cout << "len: " << length << endl;

		avg_ins = avg_ins / length;

		avg_del = avg_del / length;



		dist = dist / (double) event_aln.size();

	}

	plane->finalyze();



	return mis_per_window;	//total_num /num;

}
@@ -1108,12 +1117,12 @@ vector<str_event> Alignment::get_events_Aln() { 
//clock_t comp_aln = clock();

	std::vector<indel_str> dels;

	vector<differences_str> event_aln;

	if (Parameter::Instance()->cs_string) {

	/*	if (Parameter::Instance()->cs_string) {

	 cout<<"run cs check "<<std::endl;

	 event_aln = summarize_csstring(dels);

	} else {

	 } else {*/

	event_aln = summarizeAlignment(dels);

	}

//	}

//double time2 = Parameter::Instance()->meassure_time(comp_aln, "\tcompAln Events: ");



	vector<str_event> events;

src/ArgParseOutput.h

+3 −2
Original line number Diff line number Diff line
@@ -11,8 +11,7 @@ using std::cerr; 
using std::cout;

using std::endl;



class ArgParseOutput : public TCLAP::StdOutput

{

class ArgParseOutput: public TCLAP::StdOutput {

private:



	std::string usageStr;
@@ -36,6 +35,8 @@ public: 
		cerr << endl;

		cerr << "Short usage:" << endl;

		cerr << "       sniffles [options] -m <sorted.bam> -v <output.vcf> " << endl;

		cerr << "Version: " << Parameter::Instance()->version << std::endl;

		cerr << "Contact: fritz.sedlazeck@gmail.com" << std::endl;

		cerr << endl;

		cerr << "For complete USAGE and HELP type:" << endl;

		cerr << "    sniffles --help" << endl;