From 66be63cf810c25335b57dd232b83b18c464d2344 Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Mon, 20 Nov 2023 11:30:13 +0100
Subject: [PATCH] Rename align_(PE/SE)(_paired)

---
 src/aln.cpp | 12 ++++++------
 src/aln.hpp |  4 ++--
 src/pc.cpp  |  4 ++--
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/aln.cpp b/src/aln.cpp
index 67fd6716..424fa622 100644
--- a/src/aln.cpp
+++ b/src/aln.cpp
@@ -83,7 +83,7 @@ bool reverse_nam_if_needed(Nam& nam, const Read& read, const References& referen
     return false;
 }
 
-static inline void align_SE(
+static inline void align_single(
     const Aligner& aligner,
     Sam& sam,
     std::vector<Nam>& nams,
@@ -628,7 +628,7 @@ float top_dropoff(std::vector<Nam>& nams) {
     return 0.0;
 }
 
-inline void align_PE(
+inline void align_paired(
     const Aligner& aligner,
     Sam &sam,
     std::vector<Nam> &nams1,
@@ -967,7 +967,7 @@ void InsertSizeDistribution::update(int dist) {
     }
 }
 
-void align_PE_read(
+void align_or_map_paired(
     const KSeq &record1,
     const KSeq &record2,
     Sam& sam,
@@ -1027,7 +1027,7 @@ void align_PE_read(
                            references,
                            record2.seq.length());
     } else {
-        align_PE(aligner, sam, nams1, nams2, record1,
+        align_paired(aligner, sam, nams1, nams2, record1,
                  record2,
                  index_parameters.syncmer.k,
                  references, details,
@@ -1039,7 +1039,7 @@ void align_PE_read(
 }
 
 
-void align_SE_read(
+void align_or_map_single(
     const KSeq &record,
     Sam& sam,
     std::string &outstring,
@@ -1079,7 +1079,7 @@ void align_SE_read(
         output_hits_paf(outstring, nams, record.name, references,
                         record.seq.length());
     } else {
-        align_SE(
+        align_single(
             aligner, sam, nams, record, index_parameters.syncmer.k,
             references, details, map_param.dropoff_threshold, map_param.max_tries,
             map_param.max_secondary
diff --git a/src/aln.hpp b/src/aln.hpp
index 73f352ad..e708a24a 100644
--- a/src/aln.hpp
+++ b/src/aln.hpp
@@ -88,7 +88,7 @@ class InsertSizeDistribution {
     void update(int dist);
 };
 
-void align_PE_read(
+void align_or_map_paired(
     const klibpp::KSeq& record1,
     const klibpp::KSeq& record2,
     Sam& sam,
@@ -102,7 +102,7 @@ void align_PE_read(
     const StrobemerIndex& index
 );
 
-void align_SE_read(
+void align_or_map_single(
     const klibpp::KSeq& record,
     Sam& sam,
     std::string& outstring,
diff --git a/src/pc.cpp b/src/pc.cpp
index 32e5585e..630c42fe 100644
--- a/src/pc.cpp
+++ b/src/pc.cpp
@@ -166,13 +166,13 @@ void perform_task(
             auto record2 = records2[i];
             to_uppercase(record1.seq);
             to_uppercase(record2.seq);
-            align_PE_read(record1, record2, sam, sam_out, statistics, isize_est, aligner,
+            align_or_map_paired(record1, record2, sam, sam_out, statistics, isize_est, aligner,
                         map_param, index_parameters, references, index);
             statistics.n_reads += 2;
         }
         for (size_t i = 0; i < records3.size(); ++i) {
             auto record = records3[i];
-            align_SE_read(record, sam, sam_out, statistics, aligner, map_param, index_parameters, references, index);
+            align_or_map_single(record, sam, sam_out, statistics, aligner, map_param, index_parameters, references, index);
             statistics.n_reads++;
         }
         output_buffer.output_records(std::move(sam_out), chunk_index);