[med-svn] [Git][med-team/rna-star][upstream] New upstream version 2.6.0c+dfsg
Sascha Steinbiss
gitlab at salsa.debian.org
Wed May 16 07:45:45 BST 2018
Sascha Steinbiss pushed to branch upstream at Debian Med / rna-star
Commits:
7511af81 by Sascha Steinbiss at 2018-05-16T08:38:55+02:00
New upstream version 2.6.0c+dfsg
- - - - -
8 changed files:
- CHANGES.md
- source/Parameters.cpp
- source/ReadAlign_peOverlapMergeMap.cpp
- source/ReadAlign_waspMap.cpp
- source/STAR.cpp
- source/SequenceFuns.cpp
- source/SequenceFuns.h
- source/VERSION
Changes:
=====================================
CHANGES.md
=====================================
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,7 +1,13 @@
+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
=====================================
--- a/source/Parameters.cpp
+++ b/source/Parameters.cpp
@@ -1039,75 +1039,76 @@ void Parameters::inputParameters (int argInN, char* argIn[]) {//input parameters
pCh.out.junctions=false;
pCh.out.samOld=false;
pCh.out.bamHardClip=true;//default
- for (const auto& type1 : pCh.out.type) {
- if (type1=="WithinBAM") {
- pCh.out.bam=true;
- } else if (pCh.out.type.at(0)=="SeparateSAMold") {
- pCh.out.samOld=true;
- } else if (pCh.out.type.at(0)=="Junctions") {
- pCh.out.junctions=true;
- } else if (type1=="HardClip") {
- pCh.out.bamHardClip=true;
- } else if (type1=="SoftClip") {
- pCh.out.bamHardClip=false;
- } else {
- ostringstream errOut;
- errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --chimOutType: "<<type1 <<"\n";
- errOut <<"SOLUTION: re-run STAR with --chimOutType Junctions , SeparateSAMold , WithinBAM , HardClip \n";
- exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ 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 (type1=="SeparateSAMold") {
+ pCh.out.samOld=true;
+ } else if (type1=="Junctions") {
+ pCh.out.junctions=true;
+ } else if (type1=="HardClip") {
+ pCh.out.bamHardClip=true;
+ } else if (type1=="SoftClip") {
+ pCh.out.bamHardClip=false;
+ } else {
+ ostringstream errOut;
+ errOut <<"EXITING because of FATAL INPUT ERROR: unknown/unimplemented value for --chimOutType: "<<type1 <<"\n";
+ errOut <<"SOLUTION: re-run STAR with --chimOutType Junctions , SeparateSAMold , WithinBAM , HardClip \n";
+ exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ };
};
- };
- if (pCh.out.bam && !outBAMunsorted && !outBAMcoord) {
- ostringstream errOut;
- errOut <<"EXITING because of fatal PARAMETERS error: --chimOutType WithinBAM requires BAM output\n";
- errOut <<"SOLUTION: re-run with --outSAMtype BAM Unsorted/SortedByCoordinate\n";
- exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
- };
-
- if (pCh.multimapNmax>0 && (pCh.out.bam || pCh.out.samOld)) {
- ostringstream errOut;
- errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions\n";
- errOut <<"SOLUTION: re-run with --chimOutType Junctions\n";
- exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
- };
-
- if (peOverlap.NbasesMin > 0) {
- if (pCh.multimapNmax == 0 && (pCh.out.junctions || pCh.out.samOld)) {
+ if (pCh.out.bam && !outBAMunsorted && !outBAMcoord) {
ostringstream errOut;
- errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax 0 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType WithinBAM\n";
- errOut <<"SOLUTION: re-run with --chimOutType WithinBAM\n";
+ errOut <<"EXITING because of fatal PARAMETERS error: --chimOutType WithinBAM requires BAM output\n";
+ errOut <<"SOLUTION: re-run with --outSAMtype BAM Unsorted/SortedByCoordinate\n";
exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
};
- };
-
-
-
- if (pCh.out.bam && !outSAMattrPresent.NM) {
- outSAMattrOrder.push_back(ATTR_NM);
- inOut->logMain << "WARNING --chimOutType=WithinBAM, therefore STAR will output NM attribute" <<endl;
- };
-
- pCh.filter.genomicN=false;
- for (uint ii=0; ii<pCh.filter.stringIn.size(); ii++)
- {
- if (pCh.filter.stringIn.at(ii)=="banGenomicN")
- {
- pCh.filter.genomicN=true;
- }
- else if (pCh.filter.stringIn.at(ii)=="None")
- {//nothing to do
- }
- else
+
+ if (pCh.multimapNmax>0 && (pCh.out.bam || pCh.out.samOld)) {
+ ostringstream errOut;
+ errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax > 0 (new chimeric detection) presently only works with --chimOutType Junctions\n";
+ errOut <<"SOLUTION: re-run with --chimOutType Junctions\n";
+ exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ };
+
+ if (peOverlap.NbasesMin > 0) {
+ if (pCh.multimapNmax == 0 && (pCh.out.junctions || pCh.out.samOld)) {
+ ostringstream errOut;
+ errOut <<"EXITING because of fatal PARAMETERS error: --chimMultimapNmax 0 (default old chimeric detection) and --peOverlapNbasesMin > 0 (merging ovelrapping mates) presently only works with --chimOutType WithinBAM\n";
+ errOut <<"SOLUTION: re-run with --chimOutType WithinBAM\n";
+ exitWithError(errOut.str(), std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ };
+ };
+
+
+
+ if (pCh.out.bam && !outSAMattrPresent.NM) {
+ outSAMattrOrder.push_back(ATTR_NM);
+ inOut->logMain << "WARNING --chimOutType=WithinBAM, therefore STAR will output NM attribute" <<endl;
+ };
+
+ pCh.filter.genomicN=false;
+ for (uint ii=0; ii<pCh.filter.stringIn.size(); ii++)
{
- ostringstream errOut;
- errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --chimFilter="<<pCh.filter.stringIn.at(ii)<<"\n";
- errOut << "SOLUTION: use allowed values: banGenomicN || None";
- exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ if (pCh.filter.stringIn.at(ii)=="banGenomicN")
+ {
+ pCh.filter.genomicN=true;
+ }
+ else if (pCh.filter.stringIn.at(ii)=="None")
+ {//nothing to do
+ }
+ else
+ {
+ ostringstream errOut;
+ errOut << "EXITING because of fatal PARAMETERS error: unrecognized value of --chimFilter="<<pCh.filter.stringIn.at(ii)<<"\n";
+ errOut << "SOLUTION: use allowed values: banGenomicN || None";
+ exitWithError(errOut.str(),std::cerr, inOut->logMain, EXIT_CODE_PARAMETER, *this);
+ };
};
};
-
alignEndsType.ext[0][0]=false;
alignEndsType.ext[0][1]=false;
alignEndsType.ext[1][0]=false;
=====================================
source/ReadAlign_peOverlapMergeMap.cpp
=====================================
--- a/source/ReadAlign_peOverlapMergeMap.cpp
+++ b/source/ReadAlign_peOverlapMergeMap.cpp
@@ -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
=====================================
--- a/source/ReadAlign_waspMap.cpp
+++ b/source/ReadAlign_waspMap.cpp
@@ -61,7 +61,9 @@ void ReadAlign::waspMap() {
};
waspRA->mapOneRead();
-
+ waspRA->multMapSelect();
+ waspRA->mappedFilter();
+
if (waspRA->unmapType!=-1) {
waspType=4;
return;
=====================================
source/STAR.cpp
=====================================
--- a/source/STAR.cpp
+++ b/source/STAR.cpp
@@ -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();
=====================================
source/SequenceFuns.cpp
=====================================
--- a/source/SequenceFuns.cpp
+++ b/source/SequenceFuns.cpp
@@ -201,6 +201,32 @@ uint localSearch(const char *x, uint nx, const char *y, uint ny, double pMM){
return ixBest;
};
+uint localSearchNisMM(const char *x, uint nx, const char *y, uint ny, double pMM){
+ //find the best alignment of two short sequences x and y
+ //pMM is the maximum percentage of mismatches
+ //Ns in x OR y are considered mismatches
+ uint nMatch=0, nMM=0, nMatchBest=0, nMMbest=0, ixBest=nx;
+ for (uint ix=0;ix<nx;ix++) {
+ nMatch=0; nMM=0;
+ for (uint iy=0;iy<min(ny,nx-ix);iy++) {
+ if (x[ix+iy]==y[iy] && y[iy]<4) {
+ nMatch++;
+ } else {
+ nMM++;
+ };
+ };
+
+ if ( ( nMatch>nMatchBest || (nMatch==nMatchBest && nMM<nMMbest) ) && double(nMM)/double(nMatch)<=pMM) {
+ ixBest=ix;
+ nMatchBest=nMatch;
+ nMMbest=nMM;
+ };
+ };
+ return ixBest;
+};
+
+
+
uint qualitySplit(char* r, char* q, uint L, char Qsplit, uint maxNsplit, uint minLsplit, uint** splitR) {
//splits the read r[L] by quality scores q[L], outputs in splitR - split coordinate/length - per base
//returns number of good split regions
=====================================
source/SequenceFuns.h
=====================================
--- a/source/SequenceFuns.h
+++ b/source/SequenceFuns.h
@@ -21,6 +21,8 @@ char convertNt01234(const char R0);//transform sequence from ACGT into 0-1-2-3-
uint chrFind(uint, uint, uint*); // find chromosome from global locus
uint localSearch(const char*, uint, const char*, uint, double); //local search to clip adapter
+uint localSearchNisMM(const char *x, uint nx, const char *y, uint ny, double pMM);
+
uint qualitySplit(char*, char*, uint, char, uint, uint, uint**);
#endif
=====================================
source/VERSION
=====================================
--- a/source/VERSION
+++ b/source/VERSION
@@ -1 +1 @@
-#define STAR_VERSION "STAR_2.6.0b"
+#define STAR_VERSION "STAR_2.6.0c"
View it on GitLab: https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb
---
View it on GitLab: https://salsa.debian.org/med-team/rna-star/commit/7511af817f731678c350c9d4267755e19bc5ebbb
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