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Fix ivar filtervariants error #184

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Fix ivar filtervariants error #184

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9d7579a
Add POS_AA to read_variant_file function
LanderDC Jan 6, 2025
1f9eb4f
increase NUM_FIELDS and add POS_AA
LanderDC Jan 6, 2025
755a8bc
Write POS_AA in header
LanderDC Jan 6, 2025
114e76b
Avoid adding tab at end of tsv header
LanderDC Jan 7, 2025
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12 changes: 8 additions & 4 deletions src/get_common_variants.cpp
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#include "get_common_variants.h"

const int NUM_FIELDS = 19;
const int NUM_FIELDS = 20;
const std::string fields[NUM_FIELDS] = {
"REGION", "POS", "REF", "ALT", "REF_DP",
"REF_RV", "REF_QUAL", "ALT_DP", "ALT_RV", "ALT_QUAL",
"ALT_FREQ", "TOTAL_DP", "PVAL", "PASS", "GFF_FEATURE",
"REF_CODON", "REF_AA", "ALT_CODON", "ALT_AA"};
"REF_CODON", "REF_AA", "ALT_CODON", "ALT_AA", "POS_AA"};

const std::string na_tab_delimited_str =
"NA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA";
Expand Down Expand Up @@ -45,6 +45,7 @@ int read_variant_file(
case 16: // REF_AA
case 17: // ALT_CODON
case 18: // ALT_AA
case 19: // POS_AA
tab_delimited_key += cell + "\t";
break;
case 4:
Expand Down Expand Up @@ -103,12 +104,15 @@ int common_variants(std::string out, double min_threshold, char *files[],
for (i = 0; i < 4; ++i) {
fout << fields[i] << "\t";
}
for (i = 14; i < 19; ++i) {
for (i = 14; i < 20; ++i) {
fout << fields[i] << "\t";
}
for (i = 0; i < nfiles; ++i) {
for (j = 4; j < 14; ++j) {
fout << fields[j] << "_" << files[i] << "\t";
fout << fields[j] << "_" << files[i];
if (!(i == nfiles - 1 && j == 13)) { // Avoid adding a tab at the end
fout << "\t";
}
}
}
fout << "\n";
Expand Down