From 5a5ece2845fcad2783a5d9d04ba39c9686727025 Mon Sep 17 00:00:00 2001
From: Niema Moshiri <niemamoshiri@gmail.com>
Date: Wed, 12 Jul 2023 12:51:56 -0700
Subject: [PATCH] Fixed bug when handling insertions that are in minority count
 but have high enough count

---
 .gitignore | 10 ++++++++++
 common.h   |  2 +-
 count.cpp  | 14 ++++++++++++++
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 619aafc..66ae1e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,16 @@
 viral_consensus
 viral_consensus_debug
 
+# input files
+*.sam
+*.bam
+*.cram
+
+# output files
+*.json
+*.tsv
+*.fa
+
 # Prerequisites
 *.d
 
diff --git a/common.h b/common.h
index eac7cc4..50081f9 100644
--- a/common.h
+++ b/common.h
@@ -13,7 +13,7 @@
 #include <vector>
 
 // global definitions/constants
-#define VERSION "0.0.1"
+#define VERSION "0.0.2"
 
 // definitions/constants for argparsing
 #define DEFAULT_NUM_THREADS 1
diff --git a/count.cpp b/count.cpp
index 0994c3b..8329628 100644
--- a/count.cpp
+++ b/count.cpp
@@ -150,7 +150,21 @@ counts_t compute_counts(const char* const in_reads_fn, std::string const & ref,
                 while(pos < tmp_uint32) {
                     curr_base_qual = qqual[qpos];
                     if(curr_base_qual >= min_qual && (!primer_trim || (!is_reverse && pos >= min_max_primer_inds[src->core.pos].second) || (is_reverse && pos < min_max_primer_inds[src->core.pos].first))) {
+                        // increment the count of the base at this position
                         ++counts.pos_counts[pos][BASE_TO_NUM[(int)qseq[qpos]]];
+
+                        // increment the insertion count of "" (no insertion) after this position (except the last position)
+                        if(pos < tmp_uint32) {
+                            ins_counts_it = counts.ins_counts.find(pos);
+                            if(ins_counts_it == counts.ins_counts.end()) {
+                                ins_counts_it = counts.ins_counts.emplace(pos, std::unordered_map<std::string, COUNT_T>()).first;
+                            }
+                            ins_counts_pos_it = ins_counts_it->second.find("");
+                            if(ins_counts_pos_it == ins_counts_it->second.end()) {
+                                ins_counts_pos_it = ins_counts_it->second.emplace("", 0).first;
+                            }
+                            ++(ins_counts_pos_it->second);
+                        }
                     }
                     ++qpos; ++pos;
                 }