From 0dd90d2b77971641f9048766452a681169e58de8 Mon Sep 17 00:00:00 2001
From: rvaser <robert.vaser@fer.hr>
Date: Fri, 2 Mar 2018 17:10:50 +0100
Subject: [PATCH] Fixed catching missing sequences in input files

---
 src/main.cpp     |  2 +-
 src/overlap.cpp  |  6 +++---
 src/polisher.cpp | 10 ++++++----
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/main.cpp b/src/main.cpp
index 1ea7b5c..c60379d 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -9,7 +9,7 @@
 #include "sequence.hpp"
 #include "polisher.hpp"
 
-static const char* version = "v1.1.0";
+static const char* version = "v1.1.1";
 
 static struct option options[] = {
     {"include-unpolished", no_argument, 0, 'u'},
diff --git a/src/overlap.cpp b/src/overlap.cpp
index 119c4ed..a904f70 100644
--- a/src/overlap.cpp
+++ b/src/overlap.cpp
@@ -141,7 +141,7 @@ void Overlap::transmute(const std::unordered_map<std::string, uint64_t>& name_to
     }
 
     if (!q_name_.empty()) {
-        if (!transmuteId(name_to_id, q_name_, q_id_)) {
+        if (!transmuteId(name_to_id, q_name_ + "q", q_id_)) {
             fprintf(stderr, "[racon::Overlap::transmute] error: "
                 "missing sequence with name %s!\n", q_name_.c_str());
             exit(1);
@@ -154,7 +154,7 @@ void Overlap::transmute(const std::unordered_map<std::string, uint64_t>& name_to
         }
     }
     if (!t_name_.empty()) {
-        if (!transmuteId(name_to_id, t_name_, t_id_)) {
+        if (!transmuteId(name_to_id, t_name_ + "t", t_id_)) {
             fprintf(stderr, "[racon::Overlap::transmute] error: "
                 "missing target sequence with name %s!\n", t_name_.c_str());
             exit(1);
@@ -187,7 +187,7 @@ void Overlap::find_breaking_points(const std::vector<std::unique_ptr<Sequence>>&
         q_length_ != sequences[q_id_]->reverse_complement().size()) {
 
         fprintf(stderr, "[racon::overlap::find_breaking_points] error: "
-            "unmatched sequences lengths!\n");
+            "mismatched sequence lengths in sequence and overlap file!\n");
         exit(1);
     }
 
diff --git a/src/polisher.cpp b/src/polisher.cpp
index eb2bd5c..ce3bc6b 100644
--- a/src/polisher.cpp
+++ b/src/polisher.cpp
@@ -178,7 +178,7 @@ void Polisher::initialize() {
     std::unordered_map<std::string, uint64_t> name_to_id;
     std::unordered_map<uint64_t, uint64_t> id_to_id;
     for (uint64_t i = 0; i < targets_size; ++i) {
-        name_to_id[sequences_[i]->name()] = i;
+        name_to_id[sequences_[i]->name() + "t"] = i;
         id_to_id[i << 1 | 1] = i;
     }
 
@@ -200,7 +200,7 @@ void Polisher::initialize() {
         for (uint64_t i = l; i < sequences_.size(); ++i, ++sequences_size) {
             total_sequences_length += sequences_[i]->data().size();
 
-            auto it = name_to_id.find(sequences_[i]->name());
+            auto it = name_to_id.find(sequences_[i]->name() + "t");
             if (it != name_to_id.end()) {
                 uint64_t j = it->second;
                 if (j >= targets_size) {
@@ -218,12 +218,14 @@ void Polisher::initialize() {
                     exit(1);
                 }
 
+                name_to_id[sequences_[i]->name() + "q"] = j;
+                id_to_id[sequences_size << 1 | 0] = j;
+
                 duplicate_sequences.insert(j);
                 sequences_[i].reset();
                 ++n;
-                id_to_id[sequences_size << 1 | 0] = j;
             } else {
-                name_to_id[sequences_[i]->name()] = i - n;
+                name_to_id[sequences_[i]->name() + "q"] = i - n;
                 id_to_id[sequences_size << 1 | 0] = i - n;
             }
         }