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S3 Code Rewrite #1958

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S3 Code Rewrite #1958

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4f482c0
S3 Code Rewrite
whitwham Jul 22, 2025
fa49f59
Review changes and remove hfile_s3_write.c
whitwham Oct 23, 2025
bcbbf5b
Added more error checking.
whitwham Nov 12, 2025
00e87b0
Fixed memory leak on fail.
whitwham Nov 13, 2025
e57b07e
More tweaks.
whitwham Nov 21, 2025
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3 changes: 1 addition & 2 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Makefile for htslib, a C library for high-throughput sequencing data formats.
#
# Copyright (C) 2013-2024 Genome Research Ltd.
# Copyright (C) 2013-2025 Genome Research Ltd.
#
# Author: John Marshall <jm18@sanger.ac.uk>
#
Expand Down Expand Up @@ -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)
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5 changes: 1 addition & 4 deletions config.mk.in
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Expand Up @@ -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"
Expand All @@ -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
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1 change: 0 additions & 1 deletion hfile.c
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Expand Up @@ -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
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1 change: 0 additions & 1 deletion hfile_internal.h
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Expand Up @@ -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
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