Abstract ref_to_m5 from cram_io

.gitignore

@@ -45,6 +45,7 @@ lib*.so.*
 /test/test-vcf-api
 /test/test-vcf-sweep
 /test/test-bcf-sr
+/test/test-ref
 /test/test_view
 /test/thrash_threads[1-6]
 /test/*.tmp

Makefile

@@ -72,6 +72,7 @@ BUILT_TEST_PROGRAMS = \
 	test/hfile \
 	test/sam \
 	test/test_bgzf \
+	test/test-ref \
 	test/test-regidx \
 	test/test_view \
 	test/test-vcf-api \
@@ -154,6 +155,7 @@ LIBHTS_OBJS = \
 	multipart.o \
 	probaln.o \
 	realn.o \
+	ref.o \
 	regidx.o \
 	sam.o \
 	synced_bcf_reader.o \
@@ -326,13 +328,14 @@ plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
 probaln.o probaln.pico: probaln.c config.h $(htslib_hts_h)
 realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
 textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(hts_internal_h)
+ref.o ref.pico: ref.c config.h $(htslib_kstring_h) $(htslib_bgzf_h) $(cram_h) $(cram_io_h) $(cram_open_trace_file_h) $(htslib_hfile_h)
 
 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
 cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_endian_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
 cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
-cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
+cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_ref_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
 cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
@@ -364,7 +367,7 @@ tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htsl
 #
 # If using MSYS, avoid poor shell expansion via:
 #    MSYS2_ARG_CONV_EXCL="*" make check
-check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
+check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS) test_ebi_fetch
 	test/hts_endian
 	test/fieldarith test/fieldarith.sam
 	test/hfile
@@ -374,6 +377,18 @@ check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
 	test/test-regidx
 	cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}
 
+test_ebi_fetch:
+	export REF_CACHE=`mktemp -d` && \
+	test/test_view  -t test/xx.fa -S -C test/xx#rg.sam > test/xx#rg.tmp.cram && \
+	test/test_view -D test/xx#rg.tmp.cram > /dev/null && \
+	test/test_view -D test/xx#rg.tmp.cram > /dev/null && \
+	rm -rf $$REF_CACHE
+	export REF_CACHE=`mktemp -d` && \
+	test/test-ref && \
+	test/test-ref && \
+	rm -rf $$REF_CACHE
+
+
 test/hts_endian: test/hts_endian.o
 	$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)
 
@@ -389,6 +404,9 @@ test/sam: test/sam.o libhts.a
 test/test_bgzf: test/test_bgzf.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test_bgzf.o libhts.a -lz $(LIBS) -lpthread
 
+test/test-ref: test/test-ref.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test-ref.o libhts.a $(LIBS) -lpthread
+
 test/test-regidx: test/test-regidx.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test-regidx.o libhts.a $(LIBS) -lpthread
 
@@ -412,6 +430,7 @@ test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
 test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
 test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
 test/test_bgzf.o: test/test_bgzf.c $(htslib_bgzf_h) $(htslib_hfile_h)
+test/test-ref.o: test/test-ref.c $(htslib_bgzf_h)
 test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h) $(hts_internal_h)
 test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
 test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)