Updated follwoing review

nanoporetech · Mar 22, 2024 · 037257f · 037257f
1 parent cbdd51a
commit 037257f
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Showing 4 changed files with 4 additions and 17 deletions.
diff --git a/dorado/demux/parse_custom_sequences.cpp b/dorado/demux/parse_custom_sequences.cpp
@@ -1,28 +1,22 @@
 #include "parse_custom_sequences.h"
 
 #include "utils/bam_utils.h"
-#include "utils/barcode_kits.h"
+#include "utils/types.h"
 
 #include <htslib/sam.h>
-#include <toml.hpp>
-#include <toml/value.hpp>
-
-#include <algorithm>
-#include <string>
-#include <vector>
 
 namespace dorado::demux {
 
 std::unordered_map<std::string, std::string> parse_custom_sequences(
         const std::string& sequences_file) {
-    auto file = hts_open(sequences_file.c_str(), "r");
+    dorado::HtsFilePtr file(hts_open(sequences_file.c_str(), "r"));
     BamPtr record;
     record.reset(bam_init1());
 
     std::unordered_map<std::string, std::string> sequences;
 
     int sam_ret_val = 0;
-    while ((sam_ret_val = sam_read1(file, nullptr, record.get())) != -1) {
+    while ((sam_ret_val = sam_read1(file.get(), nullptr, record.get())) != -1) {
         if (sam_ret_val < -1) {
             throw std::runtime_error("Failed to parse custom sequence file " + sequences_file);
         }
@@ -31,8 +25,6 @@ std::unordered_map<std::string, std::string> parse_custom_sequences(
         sequences[qname] = seq;
     }
 
-    hts_close(file);
-
     return sequences;
 }
 

diff --git a/dorado/demux/parse_custom_sequences.h b/dorado/demux/parse_custom_sequences.h
@@ -1,8 +1,5 @@
 #pragma once
 
-#include "utils/barcode_kits.h"
-
-#include <optional>
 #include <string>
 #include <unordered_map>
 

diff --git a/dorado/utils/barcode_kits.cpp b/dorado/utils/barcode_kits.cpp
@@ -822,7 +822,7 @@ const std::unordered_map<std::string, KitInfo>& get_kit_infos() { return kit_inf
 
 const KitInfo* get_kit_info(const std::string& kit_name) {
     const auto& barcode_kit_infos = get_kit_infos();
-    auto kit_iter = get_kit_infos().find(kit_name);
+    auto kit_iter = barcode_kit_infos.find(kit_name);
     if (kit_iter == barcode_kit_infos.end()) {
         return nullptr;
     }

diff --git a/dorado/utils/parse_custom_kit.cpp b/dorado/utils/parse_custom_kit.cpp
@@ -1,7 +1,5 @@
 #include "parse_custom_kit.h"
 
-//#include "utils/bam_utils.h"
-//#include "utils/types.h"
 #include "utils/barcode_kits.h"
 
 #include <htslib/sam.h>