From 9381f64f3420e3e366ab4e96ea3cda792a1ff0fa Mon Sep 17 00:00:00 2001
From: Anastasia Shelestova <ashelestova@novel-soft.com>
Date: Fri, 4 Mar 2022 10:51:28 +0700
Subject: [PATCH] show all positions with adapters - got rid of fastqc diff
 adapters length bug https://github.com/smithlabcode/falco/issues/23

---
 src/FalcoConfig.cpp | 6 +++---
 src/FalcoConfig.hpp | 2 +-
 src/Module.cpp      | 4 ++--
 src/Module.hpp      | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/FalcoConfig.cpp b/src/FalcoConfig.cpp
index f1a70d6..d673011 100644
--- a/src/FalcoConfig.cpp
+++ b/src/FalcoConfig.cpp
@@ -546,13 +546,13 @@ FalcoConfig::read_adapters() {
 
       if (adapter_size == 0) {
         adapter_size = adapter_seq.size();
-        longest_adapter_size = adapter_size;
+        shortest_adapter_size = adapter_size;
       }
       else if (adapter_seq.size() != adapter_size) {
         cerr << "[adapters]\tadapters have different size. Use slow adapters search" << "\n";
         do_adapter_optimized = false;
-        if(adapter_seq.size() > longest_adapter_size){
-          longest_adapter_size = adapter_seq.size();
+        if(adapter_seq.size() < shortest_adapter_size){
+          shortest_adapter_size = adapter_seq.size();
         }
       }
 
diff --git a/src/FalcoConfig.hpp b/src/FalcoConfig.hpp
index 1cc5bdc..cf6ebf7 100644
--- a/src/FalcoConfig.hpp
+++ b/src/FalcoConfig.hpp
@@ -89,7 +89,7 @@ struct FalcoConfig {
   std::vector<size_t> adapter_hashes;
 
   size_t adapter_size;
-  size_t longest_adapter_size;
+  size_t shortest_adapter_size;
   /************************************************************
    ******* ADDITIONAL INFORMATION ABOUT THE SAMPLE ************
    ************************************************************/
diff --git a/src/Module.cpp b/src/Module.cpp
index 1589412..027f658 100644
--- a/src/Module.cpp
+++ b/src/Module.cpp
@@ -1842,7 +1842,7 @@ Module(ModuleAdapterContent::module_name) {
   adapter_names = config.adapter_names;
   adapter_seqs = config.adapter_seqs;
   adapter_hashes = config.adapter_hashes;
-  longest_adapter_size = config.longest_adapter_size; 
+  shortest_adapter_size = config.shortest_adapter_size; 
   
   // check if they are all the same size
   if (adapter_names.size() != adapter_seqs.size())
@@ -1870,7 +1870,7 @@ ModuleAdapterContent::summarize_module(FastqStats &stats) {
 
   for (size_t i = 0; i < num_adapters; ++i)
     adapter_pos_pct.push_back(
-        vector<double>(num_bases - longest_adapter_size + 1, 0.0)
+        vector<double>(num_bases - shortest_adapter_size + 1, 0.0)
     );
 
   size_t cnt;
diff --git a/src/Module.hpp b/src/Module.hpp
index ff22281..55704c9 100644
--- a/src/Module.hpp
+++ b/src/Module.hpp
@@ -340,7 +340,7 @@ class ModuleAdapterContent : public Module {
    std::vector<std::string> adapter_names;
    std::vector<std::string> adapter_seqs;
    std::vector<size_t> adapter_hashes;
-   size_t longest_adapter_size;
+   size_t shortest_adapter_size;
 
    // vector to be reported
    std::vector<std::vector<double>> adapter_pos_pct;