From af26abcaad645f153951fd103f505d01d7b35ad5 Mon Sep 17 00:00:00 2001
From: John Marshall <John.W.Marshall@glasgow.ac.uk>
Date: Thu, 5 Nov 2020 16:36:27 +0000
Subject: [PATCH] Apply HTSlib patches to fix https/S3/GCS/etc plugins

Backport symbol name typo fix; apply simplified form of upcoming
fix for samtools/htslib#1176.

Patches applicable to HTSlib 1.11; will not be needed for future
upstream versions.
---
 recipes/htslib/meta.yaml          |  4 +++-
 recipes/htslib/plugin-fixes.patch | 31 +++++++++++++++++++++++++++++++
 2 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 recipes/htslib/plugin-fixes.patch

diff --git a/recipes/htslib/meta.yaml b/recipes/htslib/meta.yaml
index d4a163527c2f0..8924147653613 100644
--- a/recipes/htslib/meta.yaml
+++ b/recipes/htslib/meta.yaml
@@ -5,13 +5,15 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('htslib', max_pin='x.x') }}
 
 source:
   url: https://github.com/samtools/htslib/releases/download/{{ version }}/htslib-{{ version }}.tar.bz2
   sha256: cffadd9baa6fce27b8fe0b01a462b489f06a5433dfe92121f667f40f632538d7
+  patches:
+    - plugin-fixes.patch
 
 requirements:
   build:
diff --git a/recipes/htslib/plugin-fixes.patch b/recipes/htslib/plugin-fixes.patch
new file mode 100644
index 0000000000000..adec848d5b11a
--- /dev/null
+++ b/recipes/htslib/plugin-fixes.patch
@@ -0,0 +1,31 @@
+Backport variable name used in dlsym typo correction.
+Revert "Link libhts.so into plugins on Unix&macOS" on macOS.
+
+diff --git a/plugin.c b/plugin.c
+index dbbe03e..d5c1981 100644
+--- a/plugin.c
++++ b/plugin.c
+@@ -153,7 +153,7 @@ plugin_void_func *load_plugin(void **pluginp, const char *filename, const char *
+         const char *basename = slash? slash+1 : filename;
+         kputsn(basename, strcspn(basename, ".-+"), &symbolg);
+ 
+-        *(void **) &sym = dlsym(lib, symbol);
++        *(void **) &sym = dlsym(lib, symbolg.s);
+         free(symbolg.s);
+         if (sym == NULL) goto error;
+     }
+diff --git a/Makefile b/Makefile
+index 245b7a1..3bb21ad 100644
+--- a/Makefile
++++ b/Makefile
+@@ -310,8 +310,8 @@ hts-object-files: $(LIBHTS_OBJS)
+ %.so: %.pico libhts.so
+ 	$(CC) -shared -Wl,-E $(LDFLAGS) -o $@ $< libhts.so $(LIBS) -lpthread
+ 
+-%.bundle: %.o libhts.dylib
+-	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< libhts.dylib $(LIBS)
++%.bundle: %.o
++	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
+ 
+ %.cygdll: %.o libhts.dll.a
+ 	$(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS)