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Variant depth issues #129

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Variant depth issues #129

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aa37eeb
print statements to trace error
cmaceves May 10, 2022
fdf2030
remove test lines, add gapped depth to variants
cmaceves May 10, 2022
cb342c7
new param specifically for gapped depth
cmaceves May 10, 2022
459a25d
removing extra test line
cmaceves May 10, 2022
59457fb
clean up
cmaceves May 10, 2022
8badc75
Merge branch 'master' into variant_depth_issues
cmaceves May 10, 2022
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2 changes: 2 additions & 0 deletions src/allele_functions.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -174,6 +174,8 @@ std::vector<allele> update_allele_depth(char ref,std::string bases, std::string
}
if(ad.size() > 0)
std::sort(ad.begin(), ad.end());
//test code
//print_allele_depths(ad);
return ad;
}

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15 changes: 13 additions & 2 deletions src/call_variants.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
<< std::endl;
int ctr = 0;
int64_t pos = 0;
uint32_t mdepth = 0, pdepth = 0; // mpdepth for mpileup depth and pdeth for ungapped depth at position
uint32_t mdepth = 0, pdepth = 0, gdepth =0; // mpdepth for mpileup depth and pdeth for ungapped depth at position
double pval_left, pval_right, pval_twotailed, *freq_depth, err;
std::stringstream line_stream;
char ref;
Expand Down Expand Up @@ -88,14 +88,19 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
}
ctr++;
}

ad = update_allele_depth(ref, bases, qualities, min_qual);
if(ad.size() == 0){
line_stream.clear();
continue;
}
// Get ungapped depth
pdepth = 0;
//get gapped depth
gdepth = 0;
for(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {
gdepth += it->depth;
//commenting these two lines gets the gapped depth
if(it->nuc[0]=='*' || it->nuc[0] == '+' || it->nuc[0] == '-')
continue;
pdepth += it->depth;
Expand All @@ -117,8 +122,14 @@ int call_variants_from_plup(std::istream &cin, std::string out_file, uint8_t min
for(std::vector<allele>::iterator it = ad.begin(); it != ad.end(); ++it) {
if((*it == *ref_it) || it->nuc[0]=='*')
continue;
freq_depth = get_frequency_depth(*it, pdepth, mdepth);
//use gapped depth if we're looking at insertion or deletion
if (it->nuc[0] == '+' || it->nuc[0] == '-'){
freq_depth = get_frequency_depth(*it, gdepth, gdepth);
}else{
freq_depth = get_frequency_depth(*it, pdepth, mdepth);
}
if(freq_depth[0] < min_threshold)

continue;
//this only adds the first bit of the information to the tsv
out_str << region << "\t";
Expand Down