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Abstract ref_to_m5 from cram_io #589

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Abstract ref_to_m5 from cram_io #589

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59dc1f9
Abstract ref_to_m5 from cram_io
ThomasHickman Jul 13, 2018
55e9668
Add error messages for failed reference lookups
ThomasHickman Jul 13, 2018
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -47,6 +47,7 @@ lib*.so.*
/test/test-regidx
/test/test-vcf-api
/test/test-vcf-sweep
/test/test-ref
/test/test_view
/test/thrash_threads[1-6]
/test/*.tmp
Expand Down
40 changes: 32 additions & 8 deletions Makefile
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Expand Up @@ -72,6 +72,7 @@ BUILT_TEST_PROGRAMS = \
test/hfile \
test/sam \
test/test_bgzf \
test/test-ref \
test/test_realn \
test/test-regidx \
test/test_view \
Expand Down Expand Up @@ -140,6 +141,7 @@ LIBHTS_OBJS = \
multipart.o \
probaln.o \
realn.o \
ref.o \
regidx.o \
sam.o \
synced_bcf_reader.o \
Expand All @@ -158,8 +160,6 @@ LIBHTS_OBJS = \
cram/cram_samtools.o \
cram/cram_stats.o \
cram/files.o \
cram/mFILE.o \
cram/open_trace_file.o \
cram/pooled_alloc.o \
cram/rANS_static.o \
cram/sam_header.o \
Expand All @@ -174,11 +174,12 @@ cram_misc_h = cram/misc.h $(cram_os_h)
cram_os_h = cram/os.h $(htslib_hts_endian_h)
cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h cram/mFILE.h $(htslib_khash_h)
cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h)
cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h $(htslib_khash_h)

hfile_internal_h = hfile_internal.h $(htslib_hfile_h) $(textutils_internal_h)
hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)
ref_internal_h = ref_internal.h $(htslib_hfile_h) cram/mFILE.h
textutils_internal_h = textutils_internal.h $(htslib_kstring_h)
thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h)

Expand Down Expand Up @@ -316,18 +317,17 @@ 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) $(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 os/lzma_stub.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 os/lzma_stub.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_ref_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)
cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.h
cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h $(cram_os_h) $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h) $(htslib_hts_log_h)
cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)
cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(htslib_hts_log_h) $(cram_sam_header_h) cram/string_alloc.h
Expand All @@ -354,7 +354,7 @@ 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
Expand All @@ -364,6 +364,26 @@ check test: $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
test/test-regidx
cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}

test_ebi_fetch:
@if [ "$(ENABLE_HTTP_TESTS)" = true ] ; then \
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Please add this script to a separate .sh file and run it from here (similarly to what has been done for the tabix test above).

export REF_CACHE=`mktemp -d` && \
echo "test ref: fetching" && \
test/test-ref && \
echo "test ref: fetch from cache" && \
test/test-ref && \
rm -rf $$REF_CACHE; \
export REF_CACHE=`mktemp -d` && \
test/test_view -t test/xx.fa -S -C test/xx#rg.sam > test/xx#rg.tmp.cram && \
echo "test view: fetching" && \
test/test_view -D test/xx#rg.tmp.cram > /dev/null && \
echo "test view: fetch from cache" && \
test/test_view -D test/xx#rg.tmp.cram > /dev/null && \
rm -rf $$REF_CACHE; \
else \
echo "Warning: testing of EBI fetching disabled"; \
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Complete the message with instructions about how to enable this test.

fi


test/hts_endian: test/hts_endian.o
$(CC) $(LDFLAGS) -o $@ test/hts_endian.o $(LIBS)

Expand All @@ -379,6 +399,9 @@ 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_realn: test/test_realn.o libhts.a
$(CC) $(LDFLAGS) -o $@ test/test_realn.o libhts.a $(LIBS) -lpthread

Expand Down Expand Up @@ -406,6 +429,7 @@ 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 config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hfile_internal_h)
test/test-realn.o: test/test_realn.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_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)
Expand Down
1 change: 1 addition & 0 deletions config.mk.in
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Expand Up @@ -47,6 +47,7 @@ LIBS = @LIBS@

PLATFORM = @PLATFORM@
PLUGIN_EXT = @PLUGIN_EXT@
ENABLE_HTTP_TESTS = @ENABLE_HTTP_TESTS@

# Lowercase here indicates these are "local" to config.mk
plugin_OBJS =
Expand Down
12 changes: 11 additions & 1 deletion configure.ac
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Expand Up @@ -136,6 +136,11 @@ AC_ARG_ENABLE([s3],
[support Amazon AWS S3 URLs])],
[], [enable_s3=check])

AC_ARG_ENABLE([http-tests],
[AS_HELP_STRING([--disable-http-tests],
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Describe the option --disable-http-tests in the Configuration section of the INSTALL file.

[disables tests that require querying to a http server])],
[disable_http_tests=yes], [disable_http_tests=no])
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@valeriuo valeriuo Dec 20, 2017 •
edited
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Also, it was decided that HTTP tests should be disabled by default. So the option should be renamed --enable-http-tests and the associated variable should only be set to true when this option is selected.

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Agreed. Although @daviesrob may have a trivial perl http server (with no complex perl package dependencies) that could permit testing against a local server without needing network access. (I'm a bit wary of going that route though unless it's very little extra code to maintain.)


test -n "$host_alias" || host_alias=unknown-`uname -s`
AC_MSG_CHECKING([shared library type for $host_alias])
case $host_alias in
Expand Down Expand Up @@ -293,10 +298,14 @@ Either configure with --without-libdeflate or resolve this error to build
HTSlib.])])])])

libcurl=disabled
ENABLE_HTTP_TESTS=false
if test "$enable_libcurl" != no; then
AC_CHECK_LIB([curl], [curl_easy_pause],
[AC_DEFINE([HAVE_LIBCURL], 1, [Define if libcurl file access is enabled.])
libcurl=enabled],
libcurl=enabled
if test "$disable_http_tests" = no; then
ENABLE_HTTP_TESTS=true
fi ],
[AC_CHECK_LIB([curl], [curl_easy_init],
[message="library is too old (7.18+ required)"],
[message="library not found"])
Expand All @@ -322,6 +331,7 @@ dnl -lcurl is only needed for static linking if hfile_libcurl is not a plugin
fi
fi
AC_SUBST([libcurl])
AC_SUBST([ENABLE_HTTP_TESTS])

gcs=disabled
if test "$enable_gcs" != no; then
Expand Down
3 changes: 0 additions & 3 deletions cram/cram_index.c
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Expand Up @@ -588,9 +588,6 @@ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
BGZF *fp;
kstring_t fn_idx_str = {0};

// Useful for cram_index_build_multiref
cram_set_option(fd, CRAM_OPT_REQUIRED_FIELDS, SAM_RNAME | SAM_POS | SAM_CIGAR);

if (! fn_idx) {
kputs(fn_base, &fn_idx_str);
kputs(".crai", &fn_idx_str);
Expand Down
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