From 251d39f057bc0a03892a0f39d7f6d89aef91070a Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sat, 19 Oct 2024 12:52:04 -0700
Subject: [PATCH] src/load_data_for_complexity.cpp: fixing a bug in checking
 whether a read is mapped -- the condition was inverted

---
 src/load_data_for_complexity.cpp | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/load_data_for_complexity.cpp b/src/load_data_for_complexity.cpp
index d8aa7a0..ed44001 100644
--- a/src/load_data_for_complexity.cpp
+++ b/src/load_data_for_complexity.cpp
@@ -520,6 +520,11 @@ load_coverage_counts_GR(const string &input_file_name, const uint64_t seed,
 #ifdef HAVE_HTSLIB
 // Deal with SAM/BAM format only if we have htslib
 
+static inline void
+is_unmapped(const bamxx::bam_rec &aln) {
+  return get_tid(aln) == -1;
+}
+
 static inline void
 swap(bamxx::bam_rec &a, bamxx::bam_rec &b) {
   std::swap(a.b, b.b);
@@ -593,12 +598,12 @@ load_counts_BAM(const uint32_t n_threads, const string &inputfile,
 
   // find first mapped read to start
   bamxx::bam_rec aln;
-  while (hts.read(hdr, aln) && get_tid(aln) == -1)
+  while (hts.read(hdr, aln) && is_unmapped(aln))
     ;
 
   size_t n_reads{};
   // if all reads unmapped, must return
-  if (get_tid(aln) == -1)
+  if (is_unmapped(aln))
     return n_reads;
 
   // to check that reads are sorted properly
@@ -611,7 +616,7 @@ load_counts_BAM(const uint32_t n_threads, const string &inputfile,
   size_t current_count = 1;
 
   while (hts.read(hdr, aln)) {
-    if (get_tid(aln) != -1)
+    if (is_unmapped(aln))
       continue;  // skip unmapped reads
 
     const aln_pos_t curr{aln};
@@ -739,11 +744,11 @@ load_coverage_counts_BAM(const uint32_t n_threads, const string &inputfile,
 
   // find first mapped read to start
   bamxx::bam_rec aln;
-  while (hts.read(hdr, aln) && get_tid(aln) == -1)
+  while (hts.read(hdr, aln) && is_unmapped(aln))
     ;
 
   size_t n_reads{};
-  if (get_tid(aln) == -1)  // no reads unmapped
+  if (is_unmapped(aln))  // no reads unmapped
     return 0;
 
   // to check reads are sorted properly
@@ -761,7 +766,7 @@ load_coverage_counts_BAM(const uint32_t n_threads, const string &inputfile,
   const hts_pos_t max_dist = bin_size + max_width;
 
   while (hts.read(hdr, aln)) {
-    if (get_tid(aln) == -1)
+    if (is_unmapped(aln))
       continue;  // check that read is mapped
 
     const hts_pos_t rlen = rlen_from_cigar(aln);