From 435e8b88b02c7e71ce70bc4c024e4191ae28428c Mon Sep 17 00:00:00 2001
From: Tim Dunn <me.timd1@gmail.com>
Date: Tue, 2 Jul 2024 16:36:53 -0400
Subject: [PATCH 1/2] fix: CMake build errors on Mac resolved

 - closes #176, CMake was including `src/utils/bedtools/gzstream/version`
   as a C++ source file, when it was a simple text file containing version info
 - I moved this version info into `src/utils/bedtools/gzstream/README`
---
 src/utils/bedtools/gzstream/README  | 2 ++
 src/utils/bedtools/gzstream/version | 1 -
 2 files changed, 2 insertions(+), 1 deletion(-)
 delete mode 100644 src/utils/bedtools/gzstream/version

diff --git a/src/utils/bedtools/gzstream/README b/src/utils/bedtools/gzstream/README
index 5fb78b2..d2fccb8 100644
--- a/src/utils/bedtools/gzstream/README
+++ b/src/utils/bedtools/gzstream/README
@@ -4,3 +4,5 @@
 ===========================================================================
 
     See index.html for documentation and installation instructions.
+
+Version 1.5 (08 Jan 2003)
diff --git a/src/utils/bedtools/gzstream/version b/src/utils/bedtools/gzstream/version
deleted file mode 100644
index 511137d..0000000
--- a/src/utils/bedtools/gzstream/version
+++ /dev/null
@@ -1 +0,0 @@
-1.5 (08 Jan 2003)

From 1260bf9f5c42c5b863d68fd1077f188f4df9d9e4 Mon Sep 17 00:00:00 2001
From: Tim Dunn <me.timd1@gmail.com>
Date: Tue, 2 Jul 2024 19:18:21 +0000
Subject: [PATCH 2/2] fix: min_intron_length_ initialization in
 JunctionsExtractor

 - fixes #188, min_intron_length_ was accidentally set from min_anchor_len_
---
 src/junctions/junctions_extractor.h | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/junctions/junctions_extractor.h b/src/junctions/junctions_extractor.h
index a95d199..0b14404 100644
--- a/src/junctions/junctions_extractor.h
+++ b/src/junctions/junctions_extractor.h
@@ -196,8 +196,23 @@ class JunctionsExtractor {
             region_ = ".";
             ref_ = "NA";
         }
-        JunctionsExtractor(string bam1, string region1, int strandness1, string strand_tag1, uint32_t min_anchor_length1, uint32_t min_intron_length1, uint32_t max_intron_length1, string ref1) : 
-            bam_(bam1), region_(region1), strandness_(strandness1), strand_tag_(strand_tag1), min_anchor_length_(min_anchor_length1), min_intron_length_(min_anchor_length1), max_intron_length_(max_intron_length1), ref_(ref1){
+        JunctionsExtractor(
+                string bam1, 
+                string region1, 
+                int strandness1, 
+                string strand_tag1, 
+                uint32_t min_anchor_length1, 
+                uint32_t min_intron_length1, 
+                uint32_t max_intron_length1, 
+                string ref1) : 
+            bam_(bam1), 
+            region_(region1), 
+            strandness_(strandness1), 
+            strand_tag_(strand_tag1), 
+            min_anchor_length_(min_anchor_length1), 
+            min_intron_length_(min_intron_length1), 
+            max_intron_length_(max_intron_length1), 
+            ref_(ref1) {
             junctions_sorted_ = false;
             output_file_ = "NA";
             output_barcodes_file_ = "NA";