int _walk_through_sam_and_split(samfile_t * fin, samfile_t **foutList)
{
bam1_t *b = bam_init1();
int r, count = 0;
while (0 <= (r = samread(fin, b))) {
if(b->core.tid > -1){
samwrite(foutList[b->core.tid], b);
}else{
samwrite(foutList[fin->header->n_targets], b);
}
count++;
}
bam_destroy1(b);
return r >= -1 ? count : -1 * count;
}
static void dump_buf(buffer_t *buf, samfile_t *out)
{
int i;
for (i = 0; i < buf->n; ++i) {
elem_t *e = buf->buf + i;
if (e->score != -1) break;
if (e->b) {
samwrite(out, e->b);
bam_destroy1(e->b);
e->b = 0;
}
}
}
int main(int argc, char* argv[]) {
samfile_t *ifile = NULL, *ofile = NULL;
bam1_t *read = bam_init1();
int keep = 0;
char *p = NULL;
//Open input file, either SAM or BAM
p = strrchr(argv[1], '.');
if(strcmp(p, ".bam") == 0) {
ifile = samopen(argv[1], "rb", NULL);
} else {
ifile = samopen(argv[1], "r", NULL);
}
bam_header_t *head = ifile->header;
//Open output file
// ofile = samopen("AND_type.bam", "wb", ifile->header);
ofile = samopen(argv[2], "wb", ifile->header);
//Iterate through the lines
while(samread(ifile, read) > 1) {
keep = 0;
//Is the read's mate on the same chromosome/contig?
if(read->core.tid == read->core.mtid) {
//Are the mates on opposite strands?
if(read->core.flag & BAM_FREVERSE && !(read->core.flag & BAM_FMREVERSE)) {
if(read->core.pos < read->core.mpos) {
// Are mates 500 bp or less from the ends?
if (read-> core.pos <= 500 && read->core.mpos > head->target_len[read->core.tid] - 500)
keep=1;
}
} else if(!(read->core.flag & BAM_FREVERSE) && read->core.flag & BAM_FMREVERSE) {
if(read->core.mpos < read->core.pos) {
if (read-> core.mpos <= 500 && read->core.pos > head->target_len[read->core.tid] - 500)
keep=1;
}
}
}
if(keep) samwrite(ofile, read);
}
bam_destroy1(read);
samclose(ifile);
samclose(ofile);
return 0;
}
void filter_by_id(const char* fn, hash_table* T)
{
fprintf(stderr, "filtering ... \n");
samfile_t* fin = samopen(fn, "rb", NULL);
if (fin == NULL) {
fprintf(stderr, "can't open bam file %s\n", fn);
exit(1);
}
samfile_t* fout = samopen("-", "w", (void*)fin->header);
if (fout == NULL) {
fprintf(stderr, "can't open stdout, for some reason.\n");
exit(1);
}
fputs(fin->header->text, stdout);
bam1_t* b = bam_init1();
uint32_t n = 0;
while (samread(fin, b) >= 0) {
if (++n % 1000000 == 0) {
fprintf(stderr, "\t%d reads\n", n);
}
if (get_hash_table(T, bam1_qname(b), b->core.l_qname) == 1) {
samwrite(fout, b);
}
}
bam_destroy1(b);
samclose(fout);
samclose(fin);
fprintf(stderr, "done.\n");
}
int
tmap_seqs_io_sff2sam_main(int argc, char *argv[])
{
int c, help = 0;
tmap_seqs_io_t *io_in = NULL;
tmap_seqs_t *seqs = NULL;
char **sam_rg = NULL;
int32_t sam_rg_num = 0;
int bidirectional = 0, sam_flowspace_tags = 0;
int out_type = 0;
tmap_sam_io_t *io_out = NULL;
bam_header_t *header = NULL; // BAM Header
int32_t i;
/*
uint8_t *key_seq = NULL;
int key_seq_len = 0;
*/
while((c = getopt(argc, argv, "DGR:Yvh")) >= 0) {
switch(c) {
case 'D': bidirectional = 1; break;
case 'G': break;
case 'R':
sam_rg = tmap_realloc(sam_rg, (1+sam_rg_num) * sizeof(char*), "sam_rg");
sam_rg[sam_rg_num] = tmap_strdup(optarg);
sam_rg_num++;
break;
case 'Y': sam_flowspace_tags = 1; break;
case 'v': tmap_progress_set_verbosity(1); break;
case 'h': help = 1; break;
default: return 1;
}
}
if(1 != argc - optind || 1 == help) {
tmap_file_fprintf(tmap_file_stderr, "Usage: %s %s [-R -Y -v -h] <in.sff>\n", PACKAGE, argv[0]);
return 1;
}
// input
io_in = tmap_seqs_io_init(&argv[optind], 1, TMAP_SEQ_TYPE_SFF, TMAP_FILE_NO_COMPRESSION, 0l, 0l);
// BAM Header
header = tmap_seqs_io_to_bam_header(NULL, io_in, sam_rg, sam_rg_num, argc, argv);
// open the output file
switch(out_type) {
case 0: // SAM
io_out = tmap_sam_io_init2("-", "wh", header);
break;
case 1:
io_out = tmap_sam_io_init2("-", "wb", header);
break;
case 2:
io_out = tmap_sam_io_init2("-", "wbu", header);
break;
default:
tmap_bug();
}
// destroy the BAM Header
bam_header_destroy(header);
header = NULL;
seqs = tmap_seqs_init(TMAP_SEQ_TYPE_SFF);
while(0 < tmap_seqs_io_read(io_in, seqs, io_out->fp->header->header)) {
bam1_t *b = NULL;
tmap_seq_t *seq = seqs->seqs[0];
b = tmap_sam_convert_unmapped(seq, sam_flowspace_tags, bidirectional, NULL,
0, 0, 0,
0, 0, 0,
"\tlq:i:%d\trq:i:%d\tla:i:%d\trq:i:%d",
seq->data.sff->rheader->clip_qual_left,
seq->data.sff->rheader->clip_qual_right,
seq->data.sff->rheader->clip_adapter_left,
seq->data.sff->rheader->clip_adapter_right);
if(samwrite(io_out->fp, b) <= 0) {
tmap_error("Error writing the SAM file", Exit, WriteFileError);
}
bam_destroy1(b);
tmap_seqs_destroy(seqs);
seqs = tmap_seqs_init(TMAP_SEQ_TYPE_SFF);
}
tmap_seqs_destroy(seqs);
// free memory
tmap_seqs_io_destroy(io_in);
tmap_sam_io_destroy(io_out);
for(i=0;i<sam_rg_num;i++) {
free(sam_rg[i]);
}
free(sam_rg);
return 0;
}
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);
}
int main () {
bam_header_t sheader;
sheader.n_targets = 2;
char testSeq1[10] = "HELLOSEQ";
char testSeq2[10] = "HELLOSE2";
sheader.target_name = (char**) malloc(sizeof(char*)*2);
sheader.target_name[0] = testSeq1;
sheader.target_name[1] = testSeq2;
sheader.target_len = (uint32_t*) malloc(sizeof(uint32_t)*2);
sheader.target_len[0] = 10;
sheader.target_len[1] = 10;
sheader.hash = NULL;
sheader.hash = NULL;
sheader.l_text=0;
sheader.text = (char*) malloc(sizeof(char)*5);
sheader.text = "@TEST";
samfile_t * sptr = samopen("ASD","wh",&sheader);
bam1_t salignment;
salignment.core.tid = 1;
salignment.core.pos = 2456;
salignment.core.bin = bam_reg2bin(0,0);
salignment.core.qual = 255; //quality
salignment.core.l_qname = 6; //lenght of the query name
salignment.core.flag = 0;
salignment.core.n_cigar = 1;
salignment.core.l_qseq = 8; //length of the read
salignment.core.mtid = 0;
salignment.core.mpos = 1357;
salignment.core.isize = 1;
salignment.l_aux = 0;
salignment.data_len = 0;
salignment.m_data = 255;
salignment.data = malloc(sizeof(uint8_t)*255);
//Name
SAMIUint8ConcatString(salignment.data,&(salignment.data_len),"QNAME",6);
//CIGAR
SAMIUint8ConcatUint32(salignment.data,&(salignment.data_len),128);
//Read
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),17);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),17);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),34);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),34);
//Quality
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
SAMIUint8ConcatUint8(salignment.data,&(salignment.data_len),0xff);
unsigned int auxStart = salignment.data_len;
SAMIUint8ConcatString(salignment.data,&(salignment.data_len),"XAZTESTING",11);
salignment.l_aux += salignment.data_len - auxStart;
//salignment.data = "QNAME\0\0\0\0\0AAAACCCC!!!!!!!!ASD";
unsigned int * asd = bam1_cigar(&salignment);
printf("%u\n",(uint32_t) (*asd));
samwrite(sptr,&salignment);
salignment.core.tid = 0;
salignment.core.pos = 1357;
samwrite(sptr,&salignment);
samclose(sptr);
return 0;
}
int bsstrand_func(bam1_t *b, const samfile_t *in, samfile_t *out, void *data) {
bsstrand_data_t *d = (bsstrand_data_t*)data;
bsstrand_conf_t *conf = d->conf;
const bam1_core_t *c = &b->core;
if (c->flag & BAM_FUNMAP){
if (out) samwrite(out, b);
d->n_unmapped++;
return 0;
}
fetch_refseq(d->rs, in->header->target_name[c->tid], c->pos, c->pos+1);
uint32_t rpos=c->pos+1, qpos=0;
int i, nC2T = 0, nG2A = 0;
uint32_t j;
char rbase, qbase;
for (i=0; i<c->n_cigar; ++i) {
uint32_t op = bam_cigar_op(bam1_cigar(b)[i]);
uint32_t oplen = bam_cigar_oplen(bam1_cigar(b)[i]);
switch(op) {
case BAM_CMATCH:
for(j=0; j<oplen; ++j) {
rbase = toupper(getbase_refseq(d->rs, rpos+j));
qbase = bscall(bam1_seq(b), qpos+j);
if (rbase == 'C' && qbase == 'T') nC2T += 1;
if (rbase == 'G' && qbase == 'A') nG2A += 1;
/* printf("%c vs %c\n", toupper(rbase), qbase); */
}
rpos += oplen;
qpos += oplen;
break;
case BAM_CINS:
qpos += oplen;
break;
case BAM_CDEL:
rpos += oplen;
break;
case BAM_CSOFT_CLIP:
qpos += oplen;
break;
default:
fprintf(stderr, "Unknown cigar, %u\n", op);
abort();
}
}
char key[2] = {'Z','S'};
unsigned char *bsstrand = bam_aux_get(b, key);
if (bsstrand) {
bsstrand++;
double s = similarity(nG2A, nC2T);
if (nG2A > 1 && nC2T > 1 && s > 0.5) {
if (conf->output_read || conf->output_all_read)
printf("F\t%s\t%d\t%d\t%d\t%s\t%s\t%1.2f\n", in->header->target_name[c->tid], c->pos, nC2T, nG2A, bam1_qname(b), bsstrand, s);
bam_aux_append(b, "OS", 'A', 1, bsstrand);
bsstrand[0] = '?';
d->n_fail++;
} else if (*bsstrand == '+' && nG2A > nC2T + 2) {
if (conf->output_read || conf->output_all_read)
printf("W2C\t%s\t%d\t%d\t%d\t%s\t%s\t%1.2f\n", in->header->target_name[c->tid], c->pos, nC2T, nG2A, bam1_qname(b), bsstrand, s);
bam_aux_append(b, "OS", 'A', 1, bsstrand);
bsstrand[0] = '-';
d->n_corr++;
} else if (*bsstrand == '-' && nC2T > nG2A + 2) {
if (conf->output_read || conf->output_all_read)
printf("C2W\t%s\t%d\t%d\t%d\t%s\t%s\t%1.2f\n", in->header->target_name[c->tid], c->pos, nC2T, nG2A, bam1_qname(b), bsstrand, s);
bam_aux_append(b, "OS", 'A', 1, bsstrand);
bsstrand[0] = '+';
d->n_corr++;
} else if (conf->output_all_read) {
printf("N\t%s\t%d\t%d\t%d\t%s\t%s\t%1.2f\n", in->header->target_name[c->tid], c->pos, nC2T, nG2A, bam1_qname(b), bsstrand, s);
}
} else if (!(c->flag & BAM_FUNMAP) && conf->infer_bsstrand) {
char bss[3];
if (similarity(nG2A, nC2T) < 0.5) {
strcpy(bss, "??");
} else if (nC2T > nG2A) {
strcpy(bss, c->flag & BAM_FREVERSE ? "+-" : "++");
} else {
strcpy(bss, c->flag & BAM_FREVERSE ? "-+" : "--");
}
bam_aux_append(b, "ZS", 'Z', 3, (uint8_t*) bss);
}
if (out) samwrite(out, b);
d->n_mapped++;
return 0;
}
void filter_by_id(const char* fn, hash_table* T)
{
fprintf(stderr, "filtering ... \n");
samfile_t* fin = samopen(fn, "rb", NULL);
if (fin == NULL) {
fprintf(stderr, "can't open bam file %s\n", fn);
exit(1);
}
samfile_t* fout = samopen("-", "w", (void*)fin->header);
if (fout == NULL) {
fprintf(stderr, "can't open stdout, for some reason.\n");
exit(1);
}
fputs(fin->header->text, stdout);
bam1_t* b = bam_init1();
uint32_t n = 0;
char* qname = NULL;
size_t qname_size = 0;
while (samread(fin, b) >= 0) {
if (++n % 1000000 == 0) {
fprintf(stderr, "\t%d reads\n", n);
}
if (qname_size < b->core.l_qname + 3) {
qname_size = b->core.l_qname + 3;
qname = realloc(qname, qname_size);
}
memcpy(qname, bam1_qname(b), b->core.l_qname);
if (b->core.flag & BAM_FREAD2) {
qname[b->core.l_qname] = '/';
qname[b->core.l_qname + 1] = '2';
qname[b->core.l_qname + 2] = '\0';
}
else {
qname[b->core.l_qname] = '/';
qname[b->core.l_qname + 1] = '1';
qname[b->core.l_qname + 2] = '\0';
}
if (get_hash_table(T, qname, b->core.l_qname + 2) == 1) {
samwrite(fout, b);
}
}
free(qname);
bam_destroy1(b);
samclose(fout);
samclose(fin);
fprintf(stderr, "done.\n");
}
