From 9d7579a623d76421e238661703879e63a8f71d92 Mon Sep 17 00:00:00 2001
From: LanderDC <75493579+LanderDC@users.noreply.github.com>
Date: Mon, 6 Jan 2025 15:58:13 +0100
Subject: [PATCH 1/4] Add POS_AA to read_variant_file function

---
 src/get_common_variants.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/get_common_variants.cpp b/src/get_common_variants.cpp
index 81248f37..0d1e6f4e 100644
--- a/src/get_common_variants.cpp
+++ b/src/get_common_variants.cpp
@@ -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:

From 1f9eb4f08b2bf112b4a073973d7ddc5a2f8507fd Mon Sep 17 00:00:00 2001
From: LanderDC <75493579+LanderDC@users.noreply.github.com>
Date: Mon, 6 Jan 2025 16:41:47 +0100
Subject: [PATCH 2/4] increase NUM_FIELDS and add POS_AA

---
 src/get_common_variants.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/get_common_variants.cpp b/src/get_common_variants.cpp
index 0d1e6f4e..bf79d454 100644
--- a/src/get_common_variants.cpp
+++ b/src/get_common_variants.cpp
@@ -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";

From 755a8bcddddb092ff5d4c504f4e4fb6999f190c1 Mon Sep 17 00:00:00 2001
From: LanderDC <75493579+LanderDC@users.noreply.github.com>
Date: Mon, 6 Jan 2025 16:54:24 +0100
Subject: [PATCH 3/4] Write POS_AA in header

---
 src/get_common_variants.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/get_common_variants.cpp b/src/get_common_variants.cpp
index bf79d454..39368402 100644
--- a/src/get_common_variants.cpp
+++ b/src/get_common_variants.cpp
@@ -104,7 +104,7 @@ 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) {

From 114e76bf2163d4983d63f41b64c3f159b4a6515d Mon Sep 17 00:00:00 2001
From: LanderDC <lander.deconinck@kuleuven.be>
Date: Tue, 7 Jan 2025 11:22:32 +0100
Subject: [PATCH 4/4] Avoid adding tab at end of tsv header

---
 src/get_common_variants.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/get_common_variants.cpp b/src/get_common_variants.cpp
index 39368402..83721980 100644
--- a/src/get_common_variants.cpp
+++ b/src/get_common_variants.cpp
@@ -109,7 +109,10 @@ int common_variants(std::string out, double min_threshold, char *files[],
   }
   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";