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minor variable name change
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jaredo committed May 5, 2017
1 parent 137fabe commit 2314a9b
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions nxtrim.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ int main(int argc,char **argv) {
pair<int,int> pos;
matePair m;
m.setAggressive(aggressive);
int nweird=0,npass=0,nread=0;
int num_reads_with_multiple_adapters=0,npass=0,nread=0;
bool trim_warn=true;

nxtrimWriter out;
Expand All @@ -181,7 +181,7 @@ int main(int argc,char **argv) {
if((!p.r1.filtered && !p.r2.filtered)||ignorePF)
{
bool weird=m.build(p,minoverlap,similarity,minlen,joinreads,hamming,preserve_mp,justmp);
nweird+=weird;
num_reads_with_multiple_adapters+=weird;
if(!weird) {
nodata+=( (m.mp.r1.l==0||m.mp.r2.l==0) && (m.pe.r1.l==0||m.pe.r2.l==0) && (m.unknown.r1.l==0||m.unknown.r2.l==0) && m.se.l==0);
se_only += ( (m.mp.r1.l==0||m.mp.r2.l==0) && (m.pe.r1.l==0||m.pe.r2.l==0) && (m.unknown.r1.l==0||m.unknown.r2.l==0) ) && m.se.l>0;
Expand All @@ -203,8 +203,8 @@ int main(int argc,char **argv) {
}
cerr << "\nTrimming summary:"<<endl;
cerr << percent(npass,nread) << "reads passed chastity/purity filters."<<endl;
cerr << percent(nweird,npass) << "reads had TWO copies of adapter (filtered)."<<endl;
npass-=nweird;
cerr << percent(num_reads_with_multiple_adapters,npass) << "reads had multiple copies of adapter (filtered)."<<endl;
npass-=num_reads_with_multiple_adapters;
cerr << percent(nodata,npass) << "read pairs were ignored because template length appeared less than read length"<<endl;
npass-=nodata;
cerr << npass << " remaining reads were trimmed"<<endl<<endl;
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