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couple of fixes to variantcaller to prevent undeclared values from be… #104

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couple of fixes to variantcaller to prevent undeclared values from be… #104

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6 changes: 3 additions & 3 deletions src/variantcaller.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -474,6 +474,8 @@ void VariantCaller::CollectMetrics() {
//fa8: moved this so we know if it is variant or not before applying the NM filter:
row.call = row.f1r2_call;
row.isvariant = VariantCaller::IsVariant(&row);
row.ismasked = VariantCaller::IsMasked(&row);
row.pyrcontext = VariantCaller::PyrimidineContext(&row);
VariantCaller::ApplyFilters(&row); // Apply filters to row
if(row.isvariant && row.f1r2_call != row.context[1] && row.f2r1_call != row.context[1]) { // fa8: these conditions are redundant
row.vaf_filter = VariantCaller::VafFilter(&row); // fa8: This one has to go separately
Expand All @@ -482,8 +484,6 @@ void VariantCaller::CollectMetrics() {
row.vaf_filter = 1;
}
if (row.pass_all_filters && row.vaf_filter) {
row.ismasked = VariantCaller::IsMasked(&row);
row.pyrcontext = VariantCaller::PyrimidineContext(&row);
this->burdens[row.ismasked][row.isvariant]++;
this->call_by_qpos[row.call][row.min_qpos][row.ismasked]++;
this->pyr_by_mask[row.pyrcontext][row.ismasked]++;
Expand Down Expand Up @@ -533,7 +533,7 @@ void VariantCaller::CollectMetrics() {
}
}
//write last line to coverage file
if(this->outfile_coverage != NULL and curr != -1 ) {
if(this->outfile_coverage != NULL and curr != -1 and cov > 0 ) {
this->gzout_coverage << lastRow.chrom;
this->gzout_coverage << "\t";
this->gzout_coverage << lastRow.chrom_beg;
Expand Down