From 17abb1bdee0e7d8322c6632c814ed8e24010d6aa Mon Sep 17 00:00:00 2001
From: Haowen Zhang <hwzhang94@gmail.com>
Date: Tue, 22 Feb 2022 22:40:07 -0500
Subject: [PATCH] Rename the variable to avoid confusion.

---
 chromap.1             | 2 +-
 src/chromap.h         | 2 +-
 src/mapping_writer.cc | 2 +-
 src/mapping_writer.h  | 6 +++---
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/chromap.1 b/chromap.1
index 6f22d4c..13b5de9 100644
--- a/chromap.1
+++ b/chromap.1
@@ -1,4 +1,4 @@
-.TH chromap 1 "22 Feb 2022" "chromap-0.2 (r353)" "Bioinformatics tools"
+.TH chromap 1 "22 Feb 2022" "chromap-0.2 (r354)" "Bioinformatics tools"
 .SH NAME
 .PP
 chromap - fast alignment and preprocessing of chromatin profiles
diff --git a/src/chromap.h b/src/chromap.h
index 2490321..4d7951d 100644
--- a/src/chromap.h
+++ b/src/chromap.h
@@ -26,7 +26,7 @@
 #include "temp_mapping.h"
 #include "utils.h"
 
-#define CHROMAP_VERSION "0.2-r353"
+#define CHROMAP_VERSION "0.2-r354"
 
 namespace chromap {
 
diff --git a/src/mapping_writer.cc b/src/mapping_writer.cc
index 9a36436..9ad6d90 100644
--- a/src/mapping_writer.cc
+++ b/src/mapping_writer.cc
@@ -378,7 +378,7 @@ void MappingWriter<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
   rid_order.resize(num_reference_sequences);
   uint32_t i;
   for (i = 0; i < num_reference_sequences; ++i) {
-    rid_order[custom_rid_rank_[i]] = i;
+    rid_order[pairs_custom_rid_rank_[i]] = i;
   }
   this->AppendMappingOutput("## pairs format v1.0.0\n#shape: upper triangle\n");
   for (i = 0; i < num_reference_sequences; ++i) {
diff --git a/src/mapping_writer.h b/src/mapping_writer.h
index 95e7147..0ab7527 100644
--- a/src/mapping_writer.h
+++ b/src/mapping_writer.h
@@ -31,10 +31,10 @@ class MappingWriter {
 
   MappingWriter(const MappingParameters mapping_parameters,
                 const uint32_t cell_barcode_length,
-                const std::vector<int> &custom_rid_rank)
+                const std::vector<int> &pairs_custom_rid_rank)
       : mapping_parameters_(mapping_parameters),
         cell_barcode_length_(cell_barcode_length),
-        custom_rid_rank_(custom_rid_rank) {
+        pairs_custom_rid_rank_(pairs_custom_rid_rank) {
     if (!mapping_parameters_.barcode_translate_table_file_path.empty()) {
       barcode_translator_.SetTranslateTable(
           mapping_parameters_.barcode_translate_table_file_path);
@@ -111,7 +111,7 @@ class MappingWriter {
   FILE *mapping_output_file_ = nullptr;
   BarcodeTranslator barcode_translator_;
   // for pairs
-  const std::vector<int> custom_rid_rank_;
+  const std::vector<int> pairs_custom_rid_rank_;
 };
 
 template <typename MappingRecord>