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added possibility of specifying file descriptors
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@grenaud
grenaud committed May 31, 2024
1 parent 25edb8b commit fea84b8
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Showing 2 changed files with 201 additions and 24 deletions.
8 changes: 8 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -145,3 +145,11 @@ src/leeHom -f AGATCGGAAGAGCACACGTCTGAACTCCAG -s GGAAGAGCGTCGTGTAGGGAAAGAGTGTAG -
```

The output files will have the `testData/outfq*` prefix.

Alternatively, you can specify the names of all 6 files:

```bash
src/leeHom -f AGATCGGAAGAGCACACGTCTGAACTCCAG -s GGAAGAGCGTCGTGTAGGGAAAGAGTGTAG --ancientdna -fq1 testData/rawAncientDNA.f1.gz -fq2 testData/rawAncientDNA.f2.gz -fqose testData/outfq.fq.gz -fqosef testData/outfq.fail.fq.gz -fqope1 testData/outfq_r1.fq.gz -fqope1f testData/outfq_r1.fail.fq.gz -fqope2 testData/outfq_r2.fq.gz -fqope2f testData/outfq_r2.fail.fq.gz
```


217 changes: 193 additions & 24 deletions src/leeHom.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1772,6 +1772,14 @@ int main (int argc, char *argv[]) {
string fastqfile2 = "";
string fastqoutfile = "";

bool fastqoutfileb=false;
string fastqoutfilese = "";
string fastqoutfilesef = "";
string fastqoutfilepe1 = "";
string fastqoutfilepe1f = "";
string fastqoutfilepe2 = "";
string fastqoutfilepe2f = "";

string intfastqoutfile = "";

bool singleEndModeFQ=true;
Expand All @@ -1787,16 +1795,27 @@ int main (int argc, char *argv[]) {

//int numberOfThreads = 1;

const string usage=string(string(argv[0])+
const string usage1=string(string(argv[0])+

" [options] BAMfile"+"\n"+
"\nThis program takes an unaligned BAM where mates are consecutive\nor fastq files and trims and merges reads\n"+

"\n\tYou can specify a unaligned bam file or one or two fastq :\n"+
"\t\t"+"-fq1 [file]" +"\t\t"+"First fastq file"+"\n"+
"\t\t"+"-fq2 [file]" +"\t\t"+"Second fastq file (for paired-end)"+"\n"+
"\t\t"+"-fqo [file]" +"\t\t"+"Output fastq prefix to file"+"\n"+
"\t\t"+"-fqt [file]" +"\t\t"+"Output interweaved fastq"+"\n\n"+
"\t\t"+"-fqo [string]" +"\t\t"+"Output fastq prefix to file (type --help for more options)"+"\n");

const string usage2=string(string("or you can use specify manually those:\n")+
"\t\t"+"-fqose [file]" +"\t\t"+"Output file for fastq single-end (or merged)"+"\n"+
"\t\t"+"-fqosef [file]" +"\t\t"+"Output file for fastq single-end (or merged) that failed"+"\n"+
"\t\t"+"-fqope1 [file]" +"\t\t"+"Output file for fastq first paired-end (or merged)"+"\n"+
"\t\t"+"-fqope1f [file]" +"\t\t"+"Output file for fastq first paired-end (or merged) that failed"+"\n"+
"\t\t"+"-fqope2 [file]" +"\t\t"+"Output file for fastq first paired-end (or merged)"+"\n"+
"\t\t"+"-fqope2f [file]" +"\t\t"+"Output file for fastq first paired-end (or merged) that failed"+"\n");


const string usage3=string(string("")+
"\t\t"+"-fqt [file]" +"\t\t"+"Output interweaved fastq"+"\n\n"+

//"\t"+"-p , --PIPE"+"\n\t\t"+"Read BAM from and write it to PIPE"+"\n"+
"\t"+"-o , --outfile" +"\t\t"+"Output (BAM format)."+"\n"+
Expand Down Expand Up @@ -1845,12 +1864,19 @@ int main (int argc, char *argv[]) {
"\t\t"+"--trimCutoff"+"\t\t\t\t"+"Lowest number of adapter bases to be observed for single Read trimming (default "+stringify(trimCutoff)+")");

if( (argc== 1) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-h") ){
cout<<"Usage:"<<endl;
cout<<""<<endl;
cout<<usage1<<usage3<<endl;
return 1;
}

if(
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cout<<"Usage:"<<endl;
cout<<""<<endl;
cout<<usage<<endl;
cout<<usage1<<usage2<<usage3<<endl;
return 1;
}

Expand Down Expand Up @@ -1910,6 +1936,62 @@ int main (int argc, char *argv[]) {
continue;
}

if(strcmp(argv[i],"-fqose") == 0 ){
fastqoutfilese=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}

if(strcmp(argv[i],"-fqosef") == 0 ){
fastqoutfilesef=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}

if(strcmp(argv[i],"-fqope1") == 0 ){
fastqoutfilepe1=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}

if(strcmp(argv[i],"-fqope1f") == 0 ){
fastqoutfilepe1f=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}

if(strcmp(argv[i],"-fqope2") == 0 ){
fastqoutfilepe2=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}

if(strcmp(argv[i],"-fqope2f") == 0 ){
fastqoutfilepe2f=string(argv[i+1]);
fastqFormat=true;
fastqoutfileb=true;
lastarg=argc;
i++;
continue;
}



if(strcmp(argv[i],"-fqt") == 0 ){
intfastqoutfile=string(argv[i+1]);
fastqFormat=true;
Expand Down Expand Up @@ -2100,15 +2182,44 @@ int main (int argc, char *argv[]) {
return 1;
}
}else{
if(!fastqoutfile.empty() && !intfastqoutfile.empty()){
cerr<<"If running in fastq input/output mode, cannot specify both -fqo and -fqt."<<endl;
int boolCfq= (!fastqoutfile.empty()) + (!intfastqoutfile.empty()) + fastqoutfileb;

if(boolCfq==0){
cerr<<"If running in fastq input/output mode, the output must specified."<<endl;
return 1;
}
if(fastqoutfile.empty() && intfastqoutfile.empty()){
cerr<<"If running in fastq input/output mode, the output must specified."<<endl;

if(boolCfq>1){
cerr<<"If running in fastq input/output mode, cannot specify both -fqo and -fqt (or the name of the 6 fastq files)."<<endl;
return 1;
}
// if(!fastqoutfile.empty() && !intfastqoutfile.empty()){
// cerr<<"If running in fastq input/output mode, cannot specify both -fqo and -fqt."<<endl;
// return 1;
// }

// if(fastqoutfile.empty() && intfastqoutfile.empty()){
// }

if(fastqoutfileb){
if(singleEndModeFQ){
boolCfq= (!fastqoutfilese.empty()) + (!fastqoutfilesef.empty());
if(boolCfq!=2){
cerr<<"If running in fastq and single-end and specifying the names of the files, 2 files have to be specified, found "<<boolCfq<<endl;
return 1;
}
}else{

boolCfq= ((!fastqoutfilese.empty()) + (!fastqoutfilesef.empty()) + (!fastqoutfilepe1.empty()) + (!fastqoutfilepe1f.empty()) + (!fastqoutfilepe2.empty()) + (!fastqoutfilepe2f.empty()));

if(boolCfq!=6){
cerr<<"If running in fastq and paired-end and specifying the names of the files, 6 files have to be specified, found "<<boolCfq<<endl;
return 1;
}

}
}

}


Expand Down Expand Up @@ -2222,17 +2333,36 @@ int main (int argc, char *argv[]) {

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(!onereadgroup.singlef->good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }

}else{
string outdirs = intfastqoutfile;
onereadgroup.single->open(outdirs.c_str(), ios::out);
onereadgroup.singlef=onereadgroup.single;

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(fastqoutfileb){

string outdirs = fastqoutfilese;
string outdirsf = fastqoutfilesef;

onereadgroup.single = new ogzstream();
onereadgroup.singlef = new ogzstream();

onereadgroup.single->open(outdirs.c_str(), ios::out);
onereadgroup.singlef->open(outdirsf.c_str(), ios::out);

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(!onereadgroup.singlef->good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }

}else{
string outdirs = intfastqoutfile;
onereadgroup.single->open(outdirs.c_str(), ios::out);
onereadgroup.singlef=onereadgroup.single;

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
}
}

}else{

fqp1 = new FastQParser (fastqfile1);
fqp2 = new FastQParser (fastqfile2);

if(!fastqoutfile.empty()){

string outdirs = fastqoutfile+".fq.gz";
Expand Down Expand Up @@ -2265,19 +2395,58 @@ int main (int argc, char *argv[]) {
if(!onereadgroup.singlef->good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }
if(!onereadgroup.pairr1f->good()){ cerr<<"Cannot write to file "<<outdir1f<<endl; return 1; }
if(!onereadgroup.pairr2f->good()){ cerr<<"Cannot write to file "<<outdir2f<<endl; return 1; }

}else{
string outdirs = intfastqoutfile;
onereadgroup.single = new ogzstream();

onereadgroup.single->open(outdirs.c_str(), ios::out);
if(fastqoutfileb){

onereadgroup.pairr1 =onereadgroup.single;
onereadgroup.pairr2 =onereadgroup.single;
onereadgroup.singlef=onereadgroup.single;
onereadgroup.pairr1f=onereadgroup.single;
onereadgroup.pairr2f=onereadgroup.single;
string outdirs = fastqoutfilese;
string outdir1 = fastqoutfilepe1;
string outdir2 = fastqoutfilepe2;

string outdirsf = fastqoutfilesef;
string outdir1f = fastqoutfilepe1f;
string outdir2f = fastqoutfilepe2f;

onereadgroup.single = new ogzstream();
onereadgroup.pairr1 = new ogzstream();
onereadgroup.pairr2 = new ogzstream();

onereadgroup.singlef = new ogzstream();
onereadgroup.pairr1f = new ogzstream();
onereadgroup.pairr2f = new ogzstream();

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
onereadgroup.single->open(outdirs.c_str(), ios::out);
onereadgroup.pairr1->open(outdir1.c_str(), ios::out);
onereadgroup.pairr2->open(outdir2.c_str(), ios::out);

onereadgroup.singlef->open(outdirsf.c_str(), ios::out);
onereadgroup.pairr1f->open(outdir1f.c_str(), ios::out);
onereadgroup.pairr2f->open(outdir2f.c_str(), ios::out);

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(!onereadgroup.pairr1->good()){ cerr<<"Cannot write to file "<<outdir1<<endl; return 1; }
if(!onereadgroup.pairr2->good()){ cerr<<"Cannot write to file "<<outdir2<<endl; return 1; }

if(!onereadgroup.singlef->good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }
if(!onereadgroup.pairr1f->good()){ cerr<<"Cannot write to file "<<outdir1f<<endl; return 1; }
if(!onereadgroup.pairr2f->good()){ cerr<<"Cannot write to file "<<outdir2f<<endl; return 1; }

}else{

string outdirs = intfastqoutfile;
onereadgroup.single = new ogzstream();

onereadgroup.single->open(outdirs.c_str(), ios::out);

onereadgroup.pairr1 =onereadgroup.single;
onereadgroup.pairr2 =onereadgroup.single;
onereadgroup.singlef=onereadgroup.single;
onereadgroup.pairr1f=onereadgroup.single;
onereadgroup.pairr2f=onereadgroup.single;

if(!onereadgroup.single->good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
}
}
}

Expand Down

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