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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.
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,31 @@ | ||
Backport variable name used in dlsym typo correction. | ||
Revert "Link libhts.so into plugins on Unix&macOS" on macOS. | ||
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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); | ||
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- *(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 | ||
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-%.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) | ||
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%.cygdll: %.o libhts.dll.a | ||
$(CC) -shared $(LDFLAGS) -o $@ $< libhts.dll.a $(LIBS) |