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splitByRG.cpp
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/*
* splitByRG
* Date: Feb-28-2013
* Author : Gabriel Renaud gabriel.reno [at sign here ] gmail.com
*
*/
#include <iostream>
#include "api/BamMultiReader.h"
#include "api/BamReader.h"
#include "api/BamWriter.h"
#include "api/BamAux.h"
#include "libgab.h"
using namespace std;
using namespace BamTools;
int main (int argc, char *argv[]) {
if( (argc!= 3) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cerr<<"Usage:splitByRG [in bam] [out prefix]"<<endl<<"this program creates one bam file per RG in the with the outprefix\nFor example splitByRG in.bam out will create\nout.rg1.bam\nout.rg2.bam\n"<<endl;
return 1;
}
string bamfiletopen = string(argv[1]);
// if(!strEndsWith(bamfiletopen,".bam")){
// }
string bamDirOutPrefix = string(argv[2]);
map<string,BamWriter *> rg2BamWriter;
// if(!isDirectory(bamDirOut)){
// cerr<<"ERROR: the out directory does not exist"<<endl;
// return 1;
// }
BamReader reader;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM files." << endl;
return 1;
}
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
vector<RefData> refData=reader.GetReferenceData();
SamReadGroupDictionary srgd=header.ReadGroups;
for(SamReadGroupConstIterator srgci=srgd.ConstBegin();
srgci<srgd.ConstEnd();
srgci++){
//cout<<*srgci<<endl;
const SamReadGroup rg = (*srgci);
//cout<<rg.ID<<endl;
rg2BamWriter[rg.ID] = new BamWriter();
rg2BamWriter[rg.ID]->Open(bamDirOutPrefix+"."+rg.ID+".bam",header,references);
}
// return 1;
// BamWriter unmapped;
// cout<<header.ToString()<<endl;
// return 1;
// if ( !unmapped.Open(bamDirOutPrefix+".unmapped.bam",header,references) ) {
// cerr << "Could not open output BAM file "<< bamDirOutPrefix+".unmapped.bam" << endl;
// return 1;
// }
BamAlignment al;
unsigned int total=0;
while ( reader.GetNextAlignment(al) ) {
// al.SetIsFailedQC(false);
// writer.SaveAlignment(al);
// if(al.IsMapped () ){
// if(rg2BamWriter.find(refData[al.RefID].RefName) == rg2BamWriter.end()){ //new
// rg2BamWriter[refData[al.RefID].RefName] = new BamWriter();
// if ( !rg2BamWriter[refData[al.RefID].RefName]->Open(bamDirOutPrefix+"."+refData[al.RefID].RefName+".bam",header,references) ) {
// cerr << "Could not open output BAM file "<< bamDirOutPrefix<<"."<<refData[al.RefID].RefName<<".bam" << endl;
// return 1;
// }
// }else{
// rg2BamWriter[refData[al.RefID].RefName]->SaveAlignment(al);
// }
// }else{
// unmapped.SaveAlignment(al);
// }
if(al.HasTag("RG")){
string rgTag;
al.GetTag("RG",rgTag);
//cout<<rgTag<<endl;
if(rg2BamWriter.find(rgTag) == rg2BamWriter.end()){ //new
cerr<<"Found new RG "<<rgTag<<endl;
rg2BamWriter[rgTag] = new BamWriter();
if ( !rg2BamWriter[rgTag]->Open(bamDirOutPrefix+"."+rgTag+".bam",header,references) ) {
cerr << "Could not open output BAM file "<< bamDirOutPrefix<<"."<<rgTag<<".bam" << endl;
return 1;
}
rg2BamWriter[rgTag]->SaveAlignment(al);
}else{
rg2BamWriter[rgTag]->SaveAlignment(al);
}
}else{
string rgTag="unknown";
//cout<<rgTag<<endl;
if(rg2BamWriter.find(rgTag) == rg2BamWriter.end()){ //new
cerr<<"Found new RG "<<rgTag<<endl;
rg2BamWriter[rgTag] = new BamWriter();
if ( !rg2BamWriter[rgTag]->Open(bamDirOutPrefix+"."+rgTag+".bam",header,references) ) {
cerr << "Could not open output BAM file "<< bamDirOutPrefix<<"."<<rgTag<<".bam" << endl;
return 1;
}
rg2BamWriter[rgTag]->SaveAlignment(al);
}else{
rg2BamWriter[rgTag]->SaveAlignment(al);
}
// cerr << "Cannot get RG tag for " << al.Name<<endl;
// return 1;
}
total++;
} //while al
reader.Close();
// writer.Close();
// unmapped.Close();
map<string,BamWriter *>::iterator rg2BamWriterIt;
for (rg2BamWriterIt =rg2BamWriter.begin();
rg2BamWriterIt!=rg2BamWriter.end();
rg2BamWriterIt++){
rg2BamWriterIt->second->Close();
}
cerr<<"Wrote succesfully "<<total<<" reads"<<endl;
return 0;
}