int main ()
{
matrix<> m1,m2;
adaptor<> bam1 (m1), bam2 (m2);
matrix_swap (bam1, bam2);
return 0;
}
void operator () (int) const {
#ifdef USE_ADAPTOR
{
#ifdef USE_BANDED
M m1 (N, N, 1, 1), m2 (N, N, 1, 1), m3 (N, N, 1, 1);
ublas::banded_adaptor<M> bam1 (m1, 1, 1), bam2 (m2, 1, 1), bam3 (m3, 1, 1);
test_with (bam1, bam2, bam3);
#ifdef USE_RANGE
ublas::matrix_range<ublas::banded_adaptor<M> > mr1 (bam1, ublas::range (0, N), ublas::range (0, N)),
mr2 (bam2, ublas::range (0, N), ublas::range (0, N)),
mr3 (bam3, ublas::range (0, N), ublas::range (0, N));
test_with (mr1, mr2, mr3);
#endif
#ifdef USE_SLICE
ublas::matrix_slice<ublas::banded_adaptor<M> > ms1 (bam1, ublas::slice (0, 1, N), ublas::slice (0, 1, N)),
ms2 (bam2, ublas::slice (0, 1, N), ublas::slice (0, 1, N)),
ms3 (bam3, ublas::slice (0, 1, N), ublas::slice (0, 1, N));
test_with (ms1, ms2, ms3);
#endif
#endif
#ifdef USE_DIAGONAL
M m1 (N, N), m2 (N, N), m3 (N, N);
ublas::diagonal_adaptor<M> dam1 (m1), dam2 (m2), dam3 (m3);
test_with (dam1, dam2, dam3);
#ifdef USE_RANGE
ublas::matrix_range<ublas::diagonal_adaptor<M> > mr1 (dam1, ublas::range (0, N), ublas::range (0, N)),
mr2 (dam2, ublas::range (0, N), ublas::range (0, N)),
mr3 (dam3, ublas::range (0, N), ublas::range (0, N));
test_with (mr1, mr2, mr3);
#endif
#ifdef USE_SLICE
ublas::matrix_slice<ublas::diagonal_adaptor<M> > ms1 (dam1, ublas::slice (0, 1, N), ublas::slice (0, 1, N)),
ms2 (dam2, ublas::slice (0, 1, N), ublas::slice (0, 1, N)),
ms3 (dam3, ublas::slice (0, 1, N), ublas::slice (0, 1, N));
test_with (ms1, ms2, ms3);
#endif
#endif
}
#endif
}
BamX::BamX(pars & Params1) // optional constructor
{
// parameters
Params=Params1;
Nread=0;
Npair=0;
Nproper=0;
Nout=0;
LFlow=INT_MIN;
LFhigh=INT_MAX;
region.limit=false;
IlluminizeBam=0;
outFragTailBam=false;
outInterChromBam=false;
outUniqueMultipleBam=false;
outUniquePartialBam=false;
outUniqueUnmappedBam=false;
outAllPairsBam=false;
outReadPairPosBam=false;
//output file
//samfile_t *fp;
bam_header_t *bam_header;
string s = Params.getInput();
BamUtil bam1(s);
Bam = bam1;
string filename=extractfilename(s);
// parameters
string fragPosFile = Params.getString("ReadPairPosFile");
string r = Params.getString("ChromRegion");
int maxReads = Params.getInt("MaxReads");
Qmin = Params.getInt("Qmin");
LRmin = Params.getInt("MinReadLength");
maxmismatchPC=Params.getDouble("FractionMaxMisMatches");
FragLengthWindow=Params.getInt("FragmentLengthWindow");
int cmd_MateMode=Params.getInt("ReadPairSenseConfig");
string ReferenceFastaFile=Params.getString("ReferenceFastaFile");
FragmentTailPercent=Params.getDouble("FragmentTailPercent");
IlluminizeBam=Params.getInt("Illuminize")>0;
outputDirectory=Params.getString("OutputDirectory");
int minLR=Params.getInt("MinReadLength");
int SplitBracketMin=Params.getInt("SplitBracketMin");
int SplitBaseQmin=Params.getInt("SplitBaseQmin");
string StatFile=Params.getString("StatFile");
if (StatFile.size()>0) {
hists H1(StatFile);
hist HLF=H1.h["LF"];
hist HLR=H1.h["LR"];
Params.setHist("LF",HLF);
Params.setHist("LR",HLR);
H1.h.clear(); // free some memory
if (FragmentTailPercent>0) {
LFlow=int(HLF.p2xTrim(FragmentTailPercent/100.));
LFhigh=int(HLF.p2xTrim(1-FragmentTailPercent/100.));
}
}
int dbg = Params.getInt("Dbg");
time(&tprev);
if (ReferenceFastaFile.size()>0) {
FastaObj RF1(ReferenceFastaFile, "");
Reference=RF1;
RF1.seq.clear(); // free some memory
}
bam_header= Bam.fp->header;
string bamheadertext = bam_header->text;
ReadGroup = extractBamTag(bamheadertext,"@RG");
outAllPairsBam=(r.size()>0);
if (!outAllPairsBam) {
outFragTailBam=true; //FragmentTailPercent>=0;
outInterChromBam=true;
outUniqueMultipleBam=true;
outUniquePartialBam=true;
outUniqueUnmappedBam=true;
}
// output Bams
outputBam.clear();
/*
// test BamHeaderContainer
vector<BamHeaderContainer> x;
string sv=SpannerVersion;
string q="@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
while (true) {
string outfile=outputDirectory+"/"+filename+".fragtail.bam";
q=q+"\n@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
BamHeaderContainer x1( bam_header, q);
x.push_back(x1);
bam_header_t* h1=x[x.size()-1].header();
cout<< h1->text << endl;
}
cout << x.size() << endl;
*/
samfile_t *fpFT=0;
samfile_t *fpIC=0;
samfile_t *fpUM=0;
samfile_t *fpUP=0;
samfile_t *fpUZ=0;
samfile_t *fpAP=0;
samfile_t *fpWP=0;
//region
if (r.size()>0) {
int r1,r2,r3;
C_region r0(r);
region=r0;
string bamRegion=region.region;
size_t k=bamRegion.find("chr");
if (k!=string::npos) {
bamRegion=bamRegion.substr(3);
}
if ( bam_parse_region(bam_header, bamRegion.c_str(), &r1, &r2, &r3)==0) {
region.limit=true;
region.anchor=r1;
region.start=r2;
region.end=r3;
} else {
cerr << "region not found\t" << r << endl;
exit(111);
}
}
//fragPosFile
if (fragPosFile.size()>0) {
FragmentPosFileObj fp(fragPosFile);
if (fp.fragmentPosList.size()>0) {
FragPos=fp;
} else {
cerr << "Read Pair Pos file not found\t" << fragPosFile << endl;
exit(112);
}
outFragTailBam=false;
outInterChromBam=false;
outUniqueMultipleBam=false;
outUniquePartialBam=false;
outUniqueUnmappedBam=false;
outReadPairPosBam=true;
}
if (outAllPairsBam) {
string outfile=outputDirectory+"/"+filename+"."+r+".bam";
string sv=SpannerVersion;
string q="@PG\tID:Region\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["AP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["AP"].header();
if ((fpAP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(160);
}
}
if (outFragTailBam) {
string outfile=outputDirectory+"/"+filename+".fragtail.bam";
string sv=SpannerVersion;
string q="@PG\tID:FragmentTail\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["FT"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["FT"].header();
if ((fpFT = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(161);
}
}
if (outInterChromBam) {
string outfile=outputDirectory+"/"+filename+".interchrom.bam";
string sv=SpannerVersion;
string q="@PG\tID:InterChromPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["IC"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["IC"].header();
if ((fpIC = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(162);
}
}
if (outUniqueMultipleBam) {
string outfile=outputDirectory+"/"+filename+".uMult.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqMultiplyMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UM"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["IUM"].header();
if ((fpUM = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(163);
}
}
if (outUniquePartialBam) {
string outfile=outputDirectory+"/"+filename+".uPart.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqPartiallyMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["UP"].header();
if ((fpUP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(164);
}
}
if (outUniqueUnmappedBam) {
string outfile=outputDirectory+"/"+filename+".uUnmapped.bam";
string sv=SpannerVersion;
string q="@PG\tID:uniqUnMappedPairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["UZ"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["UZ"].header();
if ((fpUZ = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(165);
}
}
if (outReadPairPosBam) {
string outfile=outputDirectory+"/"+filename+".weirdpairs.bam";
string sv=SpannerVersion;
string q="@PG\tID:weirdpairs\tPN:SpannerX\tVN"+sv+"\tCL:"+Params.getCmdLine();
outputBam["WP"]=BamHeaderContainer(bam_header,q);
bam_header_t* h1=outputBam["WP"].header();
if ((fpWP = samopen(outfile.c_str(), "wb", h1)) == 0) {
fprintf(stderr, "samopen: Fail to open output BAM file %s\n", filename.c_str());
exit(165);
}
}
cout << ReadGroup << endl << endl;
//extractMateMode();
if (cmd_MateMode>=0) MateMode=cmd_MateMode;
BamContainerPair bampair;
bool more = true;
while (more)
{
bampair=Bam.getNextBamPair();
// skip if neither end within region
more=(bampair.BamEnd.size()>1);
Npair++;
if (Npair>=maxReads) break;
//
if ( (dbg!=0)&&(elapsedtime()>float(dbg))) {
time(&tprev);
cout << " pairs:" << Npair << "\toutput:" << Nout;
cout << "\tchr:" << bampair.BamEnd[0].b.core.tid+1;
cout << "\tpos:" << bampair.BamEnd[0].b.core.pos;
cout << endl;
}
if (!more) continue;
if (region.limit) {
bool overlap = false;
for (int e=0; e<=1; e++) {
int a1=bampair.BamEnd[e].b.core.tid;
int p1=bampair.BamEnd[e].b.core.pos;
int p2=p1+bampair.BamEnd[e].len;
overlap=region.overlap(a1,p1,p2);
if (overlap) break;
}
if (!overlap) continue;
}
bampair.Illuminize(IlluminizeBam);
bampair.calcFragmentLengths();
more=(bampair.BamEnd[1].packeddata.size()>1);
//if (bampair.BamEnd[0].b.core.tid==bampair.BamEnd[1].b.core.tid)
// cout<< bampair << endl;
bool bothmap = ((bampair.BamEnd[0].b.core.flag&BAM_FUNMAP)==0)&&((bampair.BamEnd[0].b.core.flag&BAM_FMUNMAP)==0);
if (outAllPairsBam) {
Nout++;
int s1=samwrite(fpAP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpAP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to pairs.bam" << endl;
exit(150);
}
}
if (outReadPairPosBam) {
int ichr1=bampair.BamEnd[0].b.core.tid+1;
int istd1=bampair.BamEnd[0].sense=='+'? 0: 1;
int ista1=bampair.BamEnd[0].b.core.pos+1;
int iq1=bampair.BamEnd[0].q;
int ichr2=bampair.BamEnd[1].b.core.tid+1;
int istd2=bampair.BamEnd[1].sense=='+'? 0: 1;
int ista2=bampair.BamEnd[1].b.core.pos+1;
int iq2=bampair.BamEnd[1].q;
FragmentPosObj fp1(0,ichr1,istd1,ista1,0,ichr2,istd2,ista2,0,iq1, iq2,0);
/*
if ((fp1.chr1==10)&&(fp1.start1>=89687801)&&(fp1.end1<=89700722)) {
cout << "read "<< fp1 << endl;
}
*/
if (FragPos.find(fp1)) {
Nout++;
int s1=samwrite(fpWP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpWP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to weirdpairs.bam" << endl;
exit(156);
}
}
}
bool ok[2];
for (int e=0; e<2; e++) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[e].b));
int LR=bampair.BamEnd[0].b.core.l_qseq;
double bok=0;
for (int ib=0; ib<LR; ib++) {
if (bq[ib]>SplitBaseQmin) {
bok++;
}
}
ok[e]=(bok>LRmin);
}
if (! (ok[0]&ok[1]) )
continue;
if ( (outFragTailBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) ) {
bool FT=(bampair.FragmentLength>LFhigh)|((bampair.FragmentLength<LFlow)&(bampair.FragmentLength>INT_MIN))&bothmap;
if (FT && (fpFT!=0)) {
Nout++;
int s1=samwrite(fpFT, &(bampair.BamEnd[0].b));
int s2=samwrite(fpFT, &(bampair.BamEnd[1].b));
//if (outputBam["FT"].write(&(bampair.BamEnd[0].b),&(bampair.BamEnd[1].b))) {
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to fragtail.bam" << endl;
exit(151);
}
}
}
if ((outInterChromBam) & ((bampair.BamEnd[0].q>=Qmin)&(bampair.BamEnd[1].q>=Qmin))) {
bool IC=(bampair.BamEnd[0].b.core.tid!=bampair.BamEnd[1].b.core.tid)&&bothmap;
if (IC && (fpIC!=0)) {
Nout++;
int s1=samwrite(fpIC, &(bampair.BamEnd[0].b));
int s2=samwrite(fpIC, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to interchrom.bam" << endl;
exit(152);
}
}
}
if ((outUniqueMultipleBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin))){
int im=bampair.BamEnd[0].nmap>1? 0: 1;
int iu=bampair.BamEnd[0].q>=Qmin? 0: 1;
bool UM=(bampair.BamEnd[iu].nmap>1)&&(iu!=im)&&bothmap;
if (UM && (fpUM!=0)) {
Nout++;
int s1=samwrite(fpUM, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUM, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uMult.bam" << endl;
exit(153);
}
}
}
if ( (outUniquePartialBam) && ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) && bothmap) {
int c0=bampair.BamEnd[0].clip[0]+bampair.BamEnd[0].clip[1];
int LR=bampair.BamEnd[0].b.core.l_qseq;
bool split0=((LR-c0)>SplitBracketMin)&(c0>SplitBracketMin);
int ib0=0;
if ((split0)&(bampair.BamEnd[0].clip[0]>SplitBracketMin)) {
ib0=bampair.BamEnd[0].clip[0];
} else if ((split0)&(bampair.BamEnd[0].clip[1]>SplitBracketMin) ) {
ib0=LR-bampair.BamEnd[0].clip[1];
}
split0=split0&(ib0>0);
if (split0) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[0].b));
for (int ib=(ib0-SplitBracketMin); ib<(ib0+SplitBracketMin); ib++) {
if (bq[ib]<SplitBaseQmin) {
split0=false;
break;
}
}
}
int c1=bampair.BamEnd[1].clip[0]+bampair.BamEnd[1].clip[1];
LR=bampair.BamEnd[1].b.core.l_qseq;
bool split1=((LR-c0)>SplitBracketMin)&(c1>SplitBracketMin);;
int ib1=0;
if ((split1)&(bampair.BamEnd[1].clip[0]>SplitBracketMin)) {
ib1=bampair.BamEnd[1].clip[0];
} else if ((split1)&(bampair.BamEnd[1].clip[1]>SplitBracketMin) ) {
ib1=LR-bampair.BamEnd[1].clip[1];
}
split1=split1&(ib1>0);
if (split1) {
uint8_t* bq=bam1_qual(&(bampair.BamEnd[1].b));
for (int ib=(ib1-SplitBracketMin); ib<(ib1+SplitBracketMin); ib++) {
if (bq[ib]<SplitBaseQmin) {
split1=false;
break;
}
}
}
bool UP=(split0|split1)&((c1+c0)>minLR);
if (UP && (fpUP!=0)) {
Nout++;
int s1=samwrite(fpUP, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUP, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uPart.bam" << endl;
exit(154);
}
}
}
if ( (outUniqueUnmappedBam) & ((bampair.BamEnd[0].q>=Qmin)|(bampair.BamEnd[1].q>=Qmin)) ) {
bool z0=((bampair.BamEnd[0].b.core.flag&BAM_FUNMAP)>0);
bool z1=((bampair.BamEnd[1].b.core.flag&BAM_FUNMAP)>0);
uint8_t* bq=bam1_qual(&(bampair.BamEnd[0].b));
for (int nb,ib=0; ib<bampair.BamEnd[0].b.core.l_qseq; ib++) {
if (bq[ib]<SplitBaseQmin) {
nb++;
}
}
bool UZ=(z0|z1)&(!(z1&z0));
if (UZ && (fpUZ!=0)) {
Nout++;
int s1=samwrite(fpUZ, &(bampair.BamEnd[0].b));
int s2=samwrite(fpUZ, &(bampair.BamEnd[1].b));
if ((s1*s2)>0) {
continue;
} else {
cerr << "bad write to uUnmapped.bam" << endl;
exit(155);
}
}
}
//cout<< bampair.Orientation << "\t"<< bampair.FragmentLength << "\t" <<bampair.BamEnd[1].b.core.pos << endl;
}
if (outReadPairPosBam) {
samclose(fpWP);
} else {
if (outAllPairsBam) {
samclose(fpAP);
} else {
samclose(fpFT);
samclose(fpIC);
samclose(fpUP);
samclose(fpUM);
samclose(fpUZ);
}
}
/*
for (ioutputBam=outputBam.begin(); ioutputBam!=outputBam.end(); ioutputBam++) {
(*ioutputBam).second.close();
}
if (FragmentTailPercent>0)
outputBam["FT"].close();
*/
samclose(Bam.fp);
}
