New upstream version 2.6.0c+dfsg (7511af81) · Commits · Debian Med / rna-star

CHANGES.md

+7 −1

Original line number	Diff line number	Diff line
		STAR 2.6.0c 2018/05/10
		======================

		* Fixed bugs in merging mates (--peOverlap*) and WASP filtering algorithms. Please see CHANGES and RELEASEnotes from 2.6.0a.


		STAR 2.6.0b 2018/05/02
		======================

		* Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.5.0a.
		* Fixed bugs introduced in 2.6.0a. Please see CHANGES and RELEASEnotes from 2.6.0a.


		STAR 2.6.0a 2018/04/23

source/Parameters.cpp

+61 −60

Original line number	Diff line number	Diff line
		@@ -1039,12 +1039,13 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
		pCh.out.junctions=false;
		pCh.out.samOld=false;
		pCh.out.bamHardClip=true;//default
		if (pCh.segmentMin>0) {//only if chimeric detection is activated
		for (const auto& type1 : pCh.out.type) {
		if (type1=="WithinBAM") {
		pCh.out.bam=true;
		} else if (pCh.out.type.at(0)=="SeparateSAMold") {
		} else if (type1=="SeparateSAMold") {
		pCh.out.samOld=true;
		} else if (pCh.out.type.at(0)=="Junctions") {
		} else if (type1=="Junctions") {
		pCh.out.junctions=true;
		} else if (type1=="HardClip") {
		pCh.out.bamHardClip=true;
		@@ -1106,7 +1107,7 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
		exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
		};
		};

		};

		alignEndsType.ext[0][0]=false;
		alignEndsType.ext[0][1]=false;

source/ReadAlign_peOverlapMergeMap.cpp

+11 −15

Original line number	Diff line number	Diff line
		@@ -3,10 +3,9 @@

		void ReadAlign::peOverlapMergeMap() {


		if (!P.peOverlap.yes \|\| P.readNmates!=2 ) {//no peOverlap
		peOv.yes=false;
		return;
		peOv.yes=false;
		};

		//debug
		@@ -17,10 +16,10 @@ void ReadAlign::peOverlapMergeMap() {
		peMergeRA->copyRead(*this);
		peMergeRA->peMergeMates();
		peOv=peMergeRA->peOv;
		peOv.yes=false;

		if (peOv.nOv==0) {//check if mates can be merged, if not - return
		//cout <<"\n-1\n";
		peOv.yes=false;
		return;
		};

		@@ -36,7 +35,6 @@ void ReadAlign::peOverlapMergeMap() {
		// cout <<P.genomeNumToNT[peMergeRA->Read1[0][ii]];
		//};
		//cout << "\n";

		return;
		};

		@@ -71,10 +69,8 @@ void ReadAlign::peOverlapMergeMap() {

		//P.alignSplicedMateMapLminOverLmate=P_alignSplicedMateMapLminOverLmate;

		if (peScore<=trBest->maxScore \|\| chimRecord) {
		if (peScore<=trBest->maxScore \|\| chimRecord) {//otherwise peOv.yes=false
		peOv.yes=true;
		} else {
		peOv.yes=false;
		};

		return;
		@@ -82,8 +78,8 @@ void ReadAlign::peOverlapMergeMap() {

		void ReadAlign::peMergeMates() {

		uint s1=localSearch(Read1[0],readLength[0],Read1[0]+readLength[0]+1,readLength[1],P.peOverlap.MMp);
		uint s0=localSearch(Read1[0]+readLength[0]+1,readLength[1],Read1[0],readLength[0],P.peOverlap.MMp);
		uint s1=localSearchNisMM(Read1[0],readLength[0],Read1[0]+readLength[0]+1,readLength[1],P.peOverlap.MMp);
		uint s0=localSearchNisMM(Read1[0]+readLength[0]+1,readLength[1],Read1[0],readLength[0],P.peOverlap.MMp);

		uint o1=min(readLength[1],readLength[0]-s1);
		uint o0=min(readLength[0],readLength[1]-s0);
		@@ -203,12 +199,12 @@ void Transcript::peOverlapSEtoPE(uint* mateStart, Transcript &t) {//convert alig

		exons[nExons][EX_iFrag]=(imate==0 ? t.Str : 1-t.Str);
		exons[nExons][EX_sjA]=t.exons[iex][EX_sjA];
		if (nExons>0 && iex>0) {
		canonSJ[nExons-1]=t.canonSJ[iex-1];
		sjAnnot[nExons-1]=t.sjAnnot[iex-1];
		sjStr[nExons-1]=t.sjStr[iex-1];
		shiftSJ[nExons-1][0]=t.shiftSJ[iex-1][0];
		shiftSJ[nExons-1][1]=t.shiftSJ[iex-1][1];
		if (iex<t.nExons-1) {
		canonSJ[nExons]=t.canonSJ[iex];
		sjAnnot[nExons]=t.sjAnnot[iex];
		sjStr[nExons]=t.sjStr[iex];
		shiftSJ[nExons][0]=t.shiftSJ[iex][0];
		shiftSJ[nExons][1]=t.shiftSJ[iex][1];
		};
		//record these exons for mate2
		if (t.exons[iex][EX_R]>=mSta[imate]) {//exon left is inside the mate

source/ReadAlign_waspMap.cpp

+3 −1

Original line number	Diff line number	Diff line
		@@ -61,6 +61,8 @@ void ReadAlign::waspMap() {
		};

		waspRA->mapOneRead();
		waspRA->multMapSelect();
		waspRA->mappedFilter();

		if (waspRA->unmapType!=-1) {
		waspType=4;

source/STAR.cpp

+12 −0

Original line number	Diff line number	Diff line
		@@ -48,6 +48,18 @@ void usage() {


		int main(int argInN, char* argIn[]) {

		//debug
		// uint nn=4000000000;
		// uint* dummy=new uint[nn];
		// std::cout <<"Allocated"<<endl;
		// for (uint ii=0;ii<nn;ii++) {
		// dummy[ii]=14829735431805718528LLU;;
		// };
		// std::cout <<"Filled "<<dummy[0]<<endl;
		// delete[] dummy;
		// std::cout <<"Deleted"<<endl;

		// If no argument is given, or the first argument is either '-h' or '--help', run usage()
		if((argInN == 1) \|\| (argInN == 2 && (strcmp("-h",argIn[1]) == 0 \|\| strcmp ("--help",argIn[1]) == 0 ))) {
		usage();