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smis_sort.c
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/****************************************************************************
****************************************************************************
* *
* Copyright (C) 2013, 2014 Genome Research Ltd. *
* *
* Author: Zemin Ning ([email protected]) *
* *
* This file is part of smis_pipeline. *
* *
* ssaha_pileup is free software: you can redistribute it and/or modify it *
* under the terms of the GNU General Public License as published by the *
* Free Software Foundation, either version 3 of the License, or (at your *
* option) any later version. *
* *
* This program is distributed in the hope that it will be useful, but *
* WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU *
* General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License along *
* with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
****************************************************************************
****************************************************************************/
#include "smissv.h"
#include <api/BamReader.h>
#include <api/SamHeader.h>
#include <api/SamSequenceDictionary.h>
#include <api/BamAux.h>
#include <ctime>
using namespace BamTools;
struct ALIGNMENT {
std::string refname,readname,nmscore;
int32_t ontmask,hitrcdex,hitlocus1,hitlocus2,readl,readpos;
long int ontrdlen,ontrdidt,ontrdtag;
int superl,flag;
uint32_t hitread1,hitread2;
uint16_t mapscore;
float identy;
bool operator() (ALIGNMENT i, ALIGNMENT j) {
return( ((i.ontrdlen<<46) + (i.ontrdtag<<32) + (i.ontrdidt<<8) + i.readpos)
< ((j.ontrdlen<<46) + (j.ontrdtag<<32) + (j.ontrdidt<<8) + j.readpos));
}
} alignment;
bool notpaired(const ALIGNMENT &A)
{
if (A.flag == 1)
return true;
else
return false;
}
/*bool operator==(const ALIGNMENT& lhs, const ALIGNMENT& rhs)
{
return lhs.i == rhs.i && lhs.b == rhs.b;
}*/
static std::vector<ALIGNMENT> myaligns;
static std::vector<ALIGNMENT> finaligns;
static bool smalt=1;
struct LCONTIG {
std::string contigname;
int icontig;
bool operator() (LCONTIG i, LCONTIG j) {
return( (i.icontig) < (j.icontig) );
}
} lcontig;
static std::vector<LCONTIG> mylistcontig;
int GetIntTag(const BamAlignment &aln, const std::string &tag, unsigned long int & mytag);
int CheckTag(const BamAlignment &aln, const std::string &tag);
int ReadBwa(std::string infile);
int ReadSmalt(FILE *namef);
int Sort_and_Select();
int Sort_and_Select_forScaf();
static char nameoutscaf[100];
static char nameout[100];
static FILE *outfile;
//static FILE *namef;
static int Ncontigs;
static int Fcontigs;
static std::vector<int> finalctg;
static std::vector<std::string> sfinalctg;
static int set_score =40; // mapping score
static float set_identy=60.0; // id
static std::vector<std::string> listctg;
static int nseq=0;
static int printsome=5;
int main(int argc, char **argv)
{
int args;
int readok=-1;
FILE *namef;
time_t starttime = time(0);
std::cout << "Starting at " << starttime << std::endl;
if(argc < 2){
printf("Usage: %s [-identy 60.0] [-score 10] <alignment_file>\n",argv[0]);
exit(1);
}
args=1;
for(int i=1;i<argc;i++){
if(!strcmp(argv[i],"-score")){
sscanf(argv[++i],"%d",&set_score);
args=args+2;
}else if(!strcmp(argv[i],"-identy")){
sscanf(argv[++i],"%f",&set_identy);
args=args+2;
}
}
myaligns.reserve(100000);
std::string infile=argv[args];
std::string ftype=infile.substr(infile.size()-3);
if(ftype=="bam")
smalt=0;
if(smalt){
namef = fopen(argv[args],"r");
readok=ReadSmalt(namef);
}else{
readok=ReadBwa(infile);
}
time_t readdone = time(0);
std::cout << "Done reading at " << readdone
<< " Total time so far " << readdone-starttime<< std::endl;
if(readok == 0){
memset(nameout,'\0',100);
sprintf(nameout,"mates_id%2.0f_mscore%d.out",
set_identy,set_score);
Sort_and_Select_forScaf();
}else{
printf("\nERROR:: Alignment file not properly read!! \n");
exit(1);
}
printf("Job finished for %d reads from file %s\n",nseq,argv[args]);
time_t finish = time(0);
std::cout << "All done at " << finish
<< " Second part took " << finish-readdone
<< " sec \nTotal time " << finish-starttime << " sec"<< std::endl;
return(0);
} /* end of the main */
// ************************ //
int Sort_and_Select_forScaf()
// ************************ //
{
int i1,i2;
FILE *namef;
if((outfile = fopen(nameout,"w")) == NULL){
printf("\nERROR:: cannot write on %s \n",nameout);
exit(1);
}
// sort
std::sort(myaligns.begin(), myaligns.end(), alignment);
int cc=1;
int tot=0;
std::string prev=myaligns[0].readname;
int prevpos=0;
if(!smalt){ // Take out single reads
for(int i=0; i<myaligns.size()-1;i=i+2){
std::string thisn = myaligns[i].readname;
int thispos= myaligns[i].readpos;
std::string nextn = myaligns[i+1].readname;
int nextpos= myaligns[i+1].readpos;
if(thisn == nextn && thispos != nextpos){
finaligns.push_back(myaligns[i]);
finaligns.push_back(myaligns[i+1]);
}else{
i=i-1;
}
}
myaligns.clear();
myaligns = finaligns;
}
std::string cont1="contig183size325777";
std::string cont2="contig113size964504";
if(no)
for(int i=0; i<myaligns.size()-1;i=i+2)
if(myaligns[i].mapscore >= set_score && myaligns[i+1].mapscore >= set_score
&& (myaligns[i].identy >=set_identy) && ( myaligns[i+1].identy >= set_identy)
&& myaligns[i+1].ontmask > 0
&& (myaligns[i].refname==cont1 || myaligns[i].refname==cont2)
&& (myaligns[i+1].refname==cont1 || myaligns[i+1].refname==cont2)
&& myaligns[i].refname != myaligns[i+1].refname){
std::cout << myaligns[i].readname << "/" << myaligns[i].readpos << " "
<< myaligns[i].refname << " " << myaligns[i].identy << " " << myaligns[i].mapscore
<< " " << myaligns[i+1].readname << "/" << myaligns[i+1].readpos
<< " " << myaligns[i+1].refname << " " << myaligns[i].identy
<< " " << myaligns[i+1].mapscore << std::endl;
}
if(no)
for(int i=0; i<100;i=i+2){
std::cout << myaligns[i].readname << "/" << myaligns[i].readpos << " "
<< myaligns[i].refname << " " << myaligns[i].identy << " " << myaligns[i].mapscore
<< " " << myaligns[i+1].readname << "/" << myaligns[i+1].readpos
<< " " << myaligns[i+1].refname << " " << myaligns[i].identy
<< " " << myaligns[i+1].mapscore << std::endl;
}
listctg.erase( Unique( listctg.begin(), listctg.end() ), listctg.end() );
Ncontigs= listctg.size();
printf("Total number of contigs: %d \n", Ncontigs);
// ******
int offset1,offset2,*size_mat,*size_var,*size_head,*size_link;
char name_tag1[1000],name_tag2[1000];
if((size_mat= (int *)calloc(10,sizeof(int))) == NULL)
{
printf("ERROR Memory_Allocate: calloc - readIndex\n");
exit(1);
}
if((size_var= (int *)calloc(10,sizeof(int))) == NULL)
{
printf("ERROR Memory_Allocate: calloc - readIndex\n");
exit(1);
}
if((size_link= (int *)calloc(10,sizeof(int))) == NULL)
{
printf("ERROR Memory_Allocate: calloc - readIndex\n");
exit(1);
}
if((size_head= (int *)calloc(10,sizeof(int))) == NULL)
{
printf("ERROR Memory_Allocate: calloc - readIndex\n");
exit(1);
}
size_mat[0] = 3000;
size_mat[1] = 5000;
size_mat[2] = 7000;
size_mat[3] = 9000;
size_mat[4] = 15000;
size_mat[5] = 25000;
size_var[0] = 1000;
size_var[1] = 1000;
size_var[2] = 1000;
size_var[3] = 1000;
size_var[4] = 5000;
size_var[5] = 5000;
for(int j=0;j<myaligns.size();j++)
{
if((myaligns[j].ontrdlen <= (size_mat[0]+size_var[0])))
size_link[0]++;
if((myaligns[j].ontrdlen > (size_mat[1]-size_var[1]))&&(myaligns[j].ontrdlen <= (size_mat[1]+size_var[1])))
size_link[1]++;
if((myaligns[j].ontrdlen > (size_mat[2]-size_var[2]))&&(myaligns[j].ontrdlen <= (size_mat[2]+size_var[2])))
size_link[2]++;
if((myaligns[j].ontrdlen > (size_mat[3]-size_var[3]))&&(myaligns[j].ontrdlen <= (size_mat[3]+size_var[3])))
size_link[3]++;
if((myaligns[j].ontrdlen > (size_mat[4]-size_var[4]))&&(myaligns[j].ontrdlen <= (size_mat[4]+size_var[4])))
size_link[4]++;
if((myaligns[j].ontrdlen > (size_mat[5]-size_var[5])))
size_link[5]++;
}
size_head[0] = 0;
//printf("www: %d %d %d\n",0,size_link[0],size_head[0]);
for(int k=1;k<6;k++)
{
size_head[k] = size_head[k-1] + size_link[k-1];
//printf("www: %d %d %d\n",k,size_link[k],size_head[k]);
}
pri=0;
for(int k=0; k<6; k++)
{
int idi = size_head[k];
int idk = idi + size_link[k];
memset(nameoutscaf,'\0',100);
sprintf(nameoutscaf,"genome-matepair-%01d.dat",k);
if((namef = fopen(nameoutscaf,"w")) == NULL)
{
printf("ERROR:: cannot open %s \n",nameoutscaf);
exit(1);
}
if(no)std::cout << " total: " << myaligns.size()
<< " k " << k << " head " << size_head[k]
<< " link " << size_link[k]
<< " last " << idk
<< std::endl;
// for (int j=0; j<myaligns.size();j++){
for(int j=idi; j<idk; j++){
//if(j>364145)pri=1;
// ******
if(j%2 == 0){
i1 = j;
if(pri)std::cout << " i1 found: " << i1 << " total: " << myaligns.size() << std::endl;
}else{
i2 =j;
if(pri)std::cout << " i2 found:" << i2
<< std::endl;
if(pri)printf("cigar:%s %s %s %d %d %d %d %d %5.2f %d %d || %s %s %5.2f %d %d \n",
myaligns[i1].nmscore.c_str(),myaligns[i2].refname.c_str(), myaligns[i1].refname.c_str(),
myaligns[i1].hitread1, myaligns[i1].hitread2,
myaligns[i1].hitlocus1, myaligns[i1].hitlocus2,
myaligns[i1].hitrcdex,myaligns[i1].identy,
myaligns[i1].superl, myaligns[i1].ontrdlen,
myaligns[i1].readname.c_str(), myaligns[i2].readname.c_str(),
myaligns[i2].identy,
myaligns[i2].hitlocus1,myaligns[i2].hitlocus2);
// to avoid cases where not reading the whole alignemnt file
if( myaligns[i1].readname.substr(0,myaligns[i1].readname.length()-2)
!=myaligns[i2].readname.substr(0,myaligns[i2].readname.length()-2)){
printf("ERROR:: read mate not paired? %d %d %s %s\n",i1,i2,
myaligns[i1].readname.c_str(),
myaligns[i2].readname.c_str() );
exit(1);
}
// checkpe had wrong cut: myaligns[i1].mapscore > set_score
// change for comp!
if( (myaligns[i1].mapscore >= set_score) && (myaligns[i2].mapscore >= set_score)
&& (myaligns[i1].identy >=set_identy) && ( myaligns[i2].identy >= set_identy)
&& (myaligns[i2].ontmask > 0)) {
std::string sc = myaligns[i1].nmscore;
// change for comp!
if(myaligns[i2].mapscore < myaligns[i1].mapscore) // to be comp with smis_pipeline take this out
sc=myaligns[i2].nmscore;
int distance=0;
if((myaligns[i1].hitrcdex == 0)&&(myaligns[i2].hitrcdex == 1))
distance=myaligns[i2].hitlocus2-myaligns[i1].hitlocus1-myaligns[i2].ontrdlen;
else if((myaligns[i1].hitrcdex == 1)&&(myaligns[i2].hitrcdex == 0))
distance=myaligns[i1].hitlocus2-myaligns[i2].hitlocus1-myaligns[i2].ontrdlen;
memset(name_tag1,'\0',1000);
memset(name_tag2,'\0',1000);
if(pri)std::cout << " nametags " << std::endl;
if(myaligns[i1].hitrcdex==0)
sprintf(name_tag1,"%s %s %d %d %s","1 200 +",myaligns[i1].refname.c_str(),
myaligns[i1].hitlocus1,myaligns[i1].hitlocus1+200,"+ 200 M 200");
else
sprintf(name_tag1,"%s %s %d %d %s","200 1 -",myaligns[i1].refname.c_str(),
myaligns[i1].hitlocus2-200,myaligns[i1].hitlocus2,"+ 200 M 200");
if(myaligns[i2].hitrcdex==0)
sprintf(name_tag2,"%s %s %d %d %s","1 200 +",myaligns[i2].refname.c_str(),
myaligns[i2].hitlocus1,myaligns[i2].hitlocus1+200,"+ 200 M 200");
else
sprintf(name_tag2,"%s %s %d %d %s","200 1 -",myaligns[i2].refname.c_str(),
myaligns[i2].hitlocus2-200,myaligns[i2].hitlocus2,"+ 200 M 200");
// files used for scaffolding:
fprintf(namef,"cigar:%s %s/%d %s\n",sc.c_str(),myaligns[i1].readname.c_str(),myaligns[i1].readpos,name_tag1);
fprintf(namef,"cigar:%s %s/%d %s\n",sc.c_str(),myaligns[i2].readname.c_str(),myaligns[i2].readpos,name_tag2);
//std::cout << (sc.substr(sc.find(":")) == "A") << std::endl;
//if(sc.substr(sc.find(":")) == "A"){ // file used for structure variation analysis:
fprintf(outfile,"cigar:%s %s %s %d %d %d %d %d %5.2f %d %d || %s/%d %5.2f %d %d %d\n",
sc.c_str(),myaligns[i2].refname.c_str(), myaligns[i1].refname.c_str(),
myaligns[i1].hitread1, myaligns[i1].hitread2,
myaligns[i1].hitlocus1, myaligns[i1].hitlocus2,
myaligns[i1].hitrcdex,myaligns[i1].identy,
myaligns[i1].superl, myaligns[i1].ontrdlen,
myaligns[i2].readname.c_str(), myaligns[i2].readpos,
myaligns[i2].identy,
myaligns[i2].hitlocus1,myaligns[i2].hitlocus2,
distance);
// eliminate/reduce this next part??
std::string chr1=myaligns[i2].refname;
chr1.erase(chr1.find("size"));
int ichr1;
std::string sub;
if(chr1.size()==7)
sub = chr1.substr(chr1.size()-1, 50);
else if (chr1.size()==8)
sub = chr1.substr(chr1.size()-2, 50);
else if (chr1.size()==9)
sub = chr1.substr(chr1.size()-3, 50);
ichr1=std::atoi(sub.c_str());
finalctg.push_back(ichr1);
//}
}
}//selection
}
}
std::sort (finalctg.begin(), finalctg.end());
finalctg.erase(Unique(finalctg.begin(), finalctg.end() ),finalctg.end() );
Fcontigs= finalctg.size();
fprintf(outfile," %d %d ",Ncontigs,Fcontigs);
for(int k=0;k<Fcontigs;k++){
fprintf(outfile," %d ",finalctg[k]);
}
fprintf(outfile,"\n");
fclose(outfile);
fclose(namef);
return(0);
}
// ******************* //
int Sort_and_Select()
// ******************* //
{
int i1,i2;
if((outfile = fopen(nameout,"w")) == NULL){
printf("\nERROR:: cannot write on %s \n",nameout);
exit(1);
}
// sort
std::sort(myaligns.begin(), myaligns.end(), alignment);
listctg.erase( Unique( listctg.begin(), listctg.end() ), listctg.end() );
Ncontigs= listctg.size();
printf("Total number of contigs: %d \n", Ncontigs);
for (int j=0; j<myaligns.size();j++){
if(j%2 == 0){
i1 = j;
}else{
i2 =j;
// to avoid cases where not reading the whole alignemnt file
if( myaligns[i1].readname.substr(0,myaligns[i1].readname.length()-2)
!=myaligns[i2].readname.substr(0,myaligns[i2].readname.length()-2)){
printf("ERROR:: read mate not paired? %d %d %s %s\n",i1,i2,
myaligns[i1].readname.c_str(),
myaligns[i2].readname.c_str() );
exit(1);
}
// difference from smis_pipeline: was map_score[i1] > set_score instead of >=
if( (myaligns[i1].mapscore >= set_score) && (myaligns[i2].mapscore >= set_score)
&& (myaligns[i1].identy >=set_identy) && ( myaligns[i2].identy >= set_identy)
&& (myaligns[i2].ontmask > 0)) {
std::string sc = myaligns[i1].nmscore;
if(myaligns[i2].mapscore < myaligns[i1].mapscore)
sc=myaligns[i2].nmscore;
int distance=0;
if((myaligns[i1].hitrcdex == 0)&&(myaligns[i2].hitrcdex == 1))
distance=myaligns[i2].hitlocus2-myaligns[i1].hitlocus1-myaligns[i2].ontrdlen;
else if((myaligns[i1].hitrcdex == 1)&&(myaligns[i2].hitrcdex == 0))
distance=myaligns[i1].hitlocus2-myaligns[i2].hitlocus1-myaligns[i2].ontrdlen;
if(yes)fprintf(outfile,"cigar:%s %s %s %d %d %d %d %d %5.2f %d %d || %s %5.2f %d %d %d\n",
sc.c_str(),myaligns[i2].refname.c_str(), myaligns[i1].refname.c_str(),
myaligns[i1].hitread1, myaligns[i1].hitread2,
myaligns[i1].hitlocus1, myaligns[i1].hitlocus2,
myaligns[i1].hitrcdex,myaligns[i1].identy,
myaligns[i1].superl, myaligns[i1].ontrdlen,
myaligns[i2].readname.c_str(),
myaligns[i2].identy,
myaligns[i2].hitlocus1,myaligns[i2].hitlocus2,
distance);
// eliminate/reduce this next part??
std::string chr1=myaligns[i2].refname;
chr1.erase(chr1.find("size"));
int ichr1;
std::string sub;
if(chr1.size()==7)
sub = chr1.substr(chr1.size()-1, 50);
else if (chr1.size()==8)
sub = chr1.substr(chr1.size()-2, 50);
else if (chr1.size()==9)
sub = chr1.substr(chr1.size()-3, 50);
ichr1=std::atoi(sub.c_str());
finalctg.push_back(ichr1);
}//selection
}
}
std::sort (finalctg.begin(), finalctg.end());
finalctg.erase(Unique(finalctg.begin(), finalctg.end() ),finalctg.end() );
Fcontigs= finalctg.size();
fprintf(outfile,"%d %d ",Ncontigs,Fcontigs);
for(int k=0;k<Fcontigs;k++){
fprintf(outfile," %d ",finalctg[k]);
}
fprintf(outfile,"\n");
fclose(outfile);
return(0);
}
// ******************* //
int ReadSmalt(FILE *namef)
// ******************* //
{
int read=1;
std::string prevchr;
nseq=-1;
while(read){
if(nseq<printsome)pri=1;
else pri=0;
char nmscore[250],rname[250];
char tempc1[60],ctgname[60],nont_RC[60];
int nhit_read1,nhit_read2,nhit_locus1,nhit_locus2;
int allength,superl;
float nidenty;
ALIGNMENT thisal;
nseq++;
if(fscanf(namef,"%s %s %s %s %d %d %d %d %s %d %f %s %d %d",
nmscore,tempc1,rname,ctgname,
&nhit_read1,&nhit_read2,
&nhit_locus1,&nhit_locus2,
&nont_RC,&allength,&nidenty,
tempc1,&superl)!=EOF){
std::string thischr=ctgname;
if(prevchr!=thischr){
listctg.push_back(thischr);
prevchr=thischr;
}
// read 1 or 2
char *st;
thisal.readname = rname;
thisal.readpos = to_int(thisal.readname.substr (thisal.readname.find_last_of("/")+1));
//thisal.readname = thisal.readname.substr(0,thisal.readname.length()-2);
// Alignment Mapping score
thisal.nmscore=nmscore;
thisal.nmscore=thisal.nmscore.erase(0,10);
std::string tempstr=thisal.nmscore.substr(0,thisal.nmscore.find_last_of(":"));
thisal.mapscore = to_int(thisal.nmscore.substr (thisal.nmscore.find_last_of(":")+1));
thisal.ontmask = 0;
if(tempstr == "A")
thisal.ontmask = 1;
else if(tempstr == "D") // reads mapped in different chr or contigs, useful for scaffolding
thisal.ontmask = 2;
thisal.hitlocus1 = nhit_locus1; // leftmost pos in ref
thisal.hitlocus2 = nhit_locus2;
thisal.hitread1 = nhit_read1; // leftmost pos in ref
thisal.hitread2 = nhit_read2;
thisal.ontrdtag = to_int(thisal.readname.substr(10,6)); //insert length
thisal.ontrdlen = to_int(thisal.readname.substr(26,7));
thisal.ontrdidt = to_int(thisal.readname.substr(17,8));
thisal.superl = superl;
thisal.identy = nidenty;
thisal.refname = ctgname;
if(nont_RC[0] == 'F'){
thisal.hitrcdex = 0;
} else {
thisal.hitrcdex = 1;
}
if(no)std::cout << thisal.ontrdlen
//nmscore << " " << thisal.readname << " " << thisal.readname.substr(10,6) << " "
//<< thisal.readname.substr(17,8)
<< std::endl;
//if(nseq>100)read=0;
myaligns.push_back(thisal);
}
thisal = ALIGNMENT(); // re-initialize thisal
if(feof(namef))read=0;
}
fclose(namef);
return(0);
}
// *************************************************************************************** //
int ReadBwa(std::string infile)
// *************************************************************************************** //
{
BamReader reader;
if ( !reader.Open(infile) ) {
std::cerr << "Could not open input BAM files." << std::endl;
exit(1);
}
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
BamAlignment al;
int read=1;
std::string prevchr;
nseq=-1;
while (read && reader.GetNextAlignment(al)) {
if(nseq<printsome)pri=1;
else pri=0;
std::string strtag = "XA"; // check if read has multiple alignment
int multal=CheckTag(al,strtag);
//multal=0;
if(al.IsPrimaryAlignment() && al.IsMapped()
&& al.IsMateMapped() && !(al.AlignmentFlag & 0x800)
&& al.IsPaired() ){ //&& (multal==0 || al.MapQuality>50)){ // && al.IsProperPair()) {
//&& al.RefID == al.MateRefID){
nseq++;
std::string thischr=to_string(al.RefID);
if(prevchr!=thischr){
listctg.push_back(thischr);
prevchr=thischr;
}
ALIGNMENT thisal;
if(al.IsReverseStrand()){
thisal.hitrcdex = 1;
} else {
thisal.hitrcdex = 0;
}
thisal.mapscore = al.MapQuality;
thisal.readname = al.Name;// + "/?";
thisal.hitlocus1 = al.Position; // leftmost pos in ref
thisal.hitlocus2 = al.GetEndPosition(); // rightmost pos in ref ? or in read??? check
thisal.refname = references[al.RefID].RefName;
thisal.ontrdtag = to_int(al.Name.substr(10,6));
thisal.ontrdlen = to_int(al.Name.substr(26,7));
thisal.ontrdidt = to_int(al.Name.substr(17,8));
thisal.readl = al.Length;
//if(multal)
thisal.flag=1;
thisal.readpos = 1;
if(al.IsSecondMate())thisal.readpos = 2;
strtag = "NM";
unsigned long int value;
if(GetIntTag(al,strtag,value)){
printf("WARNING:: cannot find \"NM\" field in your bam file, each read identity will be set to 99\% \n");
value=al.AlignedBases.size()-1;
}
thisal.identy = (value*100.) /(al.AlignedBases.size());
//ctgname no need
//ont_RC[i] no need
//superlength[i]) not needed?
// not defined in bwa
thisal.hitread1 = 0; // leftmost pos in read
thisal.hitread2 = 0; // rigthmost pos in read
thisal.ontmask = 1; // A cut: only properly paired reads
if(al.RefID != al.MateRefID)
thisal.nmscore= "D:"+ to_string(thisal.mapscore);
else
thisal.nmscore= "A:"+ to_string(thisal.mapscore);
thisal.superl=0; //superlength[i]) not needed?
if(no) std::cout << " reading " << thisal.readname
<< " " << thisal.readpos << std::endl;
if(no)std::cout << " flag " << al.AlignmentFlag << std::endl
<< " 0x1 " << (al.AlignmentFlag & 0x1) << std::endl
<< " 0x2 " << (al.AlignmentFlag & 0x2) << std::endl
<< " 0x4 " << (al.AlignmentFlag & 0x4) << std::endl
<< " 0x8 " << (al.AlignmentFlag & 0x8) << std::endl
<< " 0x10 " << (al.AlignmentFlag & 0x10) << std::endl
<< " 0x20 " << (al.AlignmentFlag & 0x20) << std::endl
<< " 0x40 " << (al.AlignmentFlag & 0x40) << std::endl
<< " 0x80 " << (al.AlignmentFlag & 0x80) << std::endl
<< " 0x100 " << (al.AlignmentFlag & 0x100) << std::endl
<< " 0x200 " << (al.AlignmentFlag & 0x200) << std::endl
<< " 0x400 " << (al.AlignmentFlag & 0x400) << std::endl
<< " 0x800 " << (al.AlignmentFlag & 0x800) << std::endl;
myaligns.push_back(thisal);
thisal = ALIGNMENT(); // re-initialize thisal
}//selection
//if(nseq>5)read=0;
}//while
return(0);
}
// *************************************************************************************** //
int GetIntTag(const BamAlignment &aln, const std::string &tag, unsigned long int & mytag){
// *************************************************************************************** //
char type;
uint32_t val;
if (!aln.HasTag(tag)){
std::cout << "ERROR:: no tag found " << std::endl;
return(1);
}
if (!aln.GetTagType(tag,type)){
std::cout << "ERROR:: tag " << tag << " not found " << std::endl;
return(2);
}
if(aln.GetTag(tag,val)){
mytag = val;
return(0);
}else{
std::cout << "ERROR:: tag " << tag << " has wrong format " << std::endl;
return(3);
}
}
// *************************************************************************************** //
int CheckTag(const BamAlignment &aln, const std::string &tag){
// *************************************************************************************** //
char type;
std::string val;
if (!aln.HasTag(tag)){
// fine: no tag
return(0);
}else{
return(1);
}
}