S3 Code Rewrite (PR #1958)

Add code to read from S3 sources in the same style as the current writing code.
Merge the s3_write.c code into hfile_s3.c to put all the S3 code in the same
file.

This should simplify the S3 code and give us a little more flexibility in how
we use it.

Author: whitwham

Makefile

@@ -500,7 +500,6 @@ header.o header.pico: header.c config.h $(textutils_internal_h) $(header_h) $(ht
 hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(htslib_kstring_h) $(hts_internal_h) $(htslib_khash_h)
 hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)
 hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
-hfile_s3_write.o hfile_s3_write.pico: hfile_s3_write.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
 hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(hts_time_funcs_h)
 hts.o hts.pico: hts.c config.h os/lzma_stub.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_hts_endian_h) version.h config_vars.h $(hts_internal_h) $(hfile_internal_h) $(sam_internal_h) $(htslib_hts_expr_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(htslib_tbx_h) $(htscodecs_htscodecs_h)
 hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(htslib_hts_log_h) $(textutils_internal_h)

config.mk.in

@@ -79,12 +79,10 @@ endif
 
 ifeq "s3-@s3@" "s3-enabled"
 plugin_OBJS += hfile_s3.o
-plugin_OBJS += hfile_s3_write.o
 
 CRYPTO_LIBS = @CRYPTO_LIBS@
 noplugin_LIBS += $(CRYPTO_LIBS)
-hfile_s3$(PLUGIN_EXT): LIBS += $(CRYPTO_LIBS)
-hfile_s3_write$(PLUGIN_EXT): LIBS += $(CRYPTO_LIBS) $(LIBCURL_LIBS)
+hfile_s3$(PLUGIN_EXT): LIBS += $(CRYPTO_LIBS) $(LIBCURL_LIBS)
 endif
 
 ifeq "plugins-@enable_plugins@" "plugins-yes"
@@ -101,7 +99,6 @@ plugin.o plugin.pico: ALL_CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
 hfile_gcs.o hfile_gcs.pico: version.h
 hfile_libcurl.o hfile_libcurl.pico: version.h
 hfile_s3.o hfile_s3.pico: version.h
-hfile_s3_write.o hfile_s3_write.pico: version.h
 
 # Windows DLL plugins depend on the import library, built as a byproduct.
 $(plugin_OBJS:.o=.cygdll): cyghts-$(LIBHTS_SOVERSION).dll

hfile.c

@@ -1136,7 +1136,6 @@ static int load_hfile_plugins(void)
 #endif
 #ifdef ENABLE_S3
     init_add_plugin(NULL, hfile_plugin_init_s3, "s3");
-    init_add_plugin(NULL, hfile_plugin_init_s3_write, "s3w");
 #endif
 
 #endif

hfile_internal.h

@@ -182,7 +182,6 @@ extern int hfile_plugin_init(struct hFILE_plugin *self);
 extern int hfile_plugin_init_gcs(struct hFILE_plugin *self);
 extern int hfile_plugin_init_libcurl(struct hFILE_plugin *self);
 extern int hfile_plugin_init_s3(struct hFILE_plugin *self);
-extern int hfile_plugin_init_s3_write(struct hFILE_plugin *self);
 #endif
 
 // Callback to allow headers to be set in http connections.  Currently used