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Miscellaneous trivia and minor fixes #1705

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merged 5 commits into from
Nov 27, 2023
Merged

Miscellaneous trivia and minor fixes #1705

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a51190a
Remove remnants of HTS_HAVE_NEON, unused since PR #1587
jmarshall Aug 16, 2023
54a02fa
Remove NUMERIC_VERSION, unused since PR #1226
jmarshall Aug 19, 2023
1f467ca
Document primarily MM/ML and fix base-mod-related typos
jmarshall Nov 11, 2023
2472490
Compare as off_t (not size_t) and fix printf specifiers
jmarshall Nov 24, 2023
958e704
Install annot-tsv.1 man page and alphabetise annot-tsv rules
jmarshall Nov 24, 2023
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20 changes: 7 additions & 13 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -68,10 +68,10 @@ INSTALL_PROGRAM = $(INSTALL)
plugindir =

BUILT_PROGRAMS = \
annot-tsv \
bgzip \
htsfile \
tabix \
annot-tsv
tabix

BUILT_TEST_PROGRAMS = \
test/hts_endian \
Expand Down Expand Up @@ -153,10 +153,6 @@ LIBHTS_SOVERSION = 3
MACH_O_COMPATIBILITY_VERSION = 3.1.18
MACH_O_CURRENT_VERSION = 3.1.18

# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
# even if this is a dirty or untagged Git working tree.
NUMERIC_VERSION := $(shell $(srcdir)/version.sh numeric)

# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))

Expand All @@ -168,7 +164,6 @@ print-version:

show-version:
@echo PACKAGE_VERSION = $(PACKAGE_VERSION)
@echo NUMERIC_VERSION = $(NUMERIC_VERSION)

config_vars.h: override escape=$(subst ',\x27,$(subst ",\",$(subst \,\\,$(1))))
config_vars.h: override hts_cc_escaped=$(call escape,$(CC))
Expand Down Expand Up @@ -352,7 +347,6 @@ print-config:
@echo HTS_CFLAGS_AVX2 = $(HTS_CFLAGS_AVX2)
@echo HTS_CFLAGS_AVX512 = $(HTS_CFLAGS_AVX512)
@echo HTS_CFLAGS_SSE4 = $(HTS_CFLAGS_SSE4)
@echo HTS_HAVE_NEON = $(HTS_HAVE_NEON)
@echo LDFLAGS = $(LDFLAGS)
@echo LIBHTS_OBJS = $(LIBHTS_OBJS)
@echo LIBS = $(LIBS)
Expand Down Expand Up @@ -506,6 +500,9 @@ htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x
htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico: TARGET_CFLAGS = $(HTS_CFLAGS_AVX512)
htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico: TARGET_CFLAGS = $(HTS_CFLAGS_SSE4)

annot-tsv: annot-tsv.o libhts.a
$(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread

bgzip: bgzip.o libhts.a
$(CC) $(LDFLAGS) -o $@ bgzip.o libhts.a $(LIBS) -lpthread

Expand All @@ -515,13 +512,10 @@ htsfile: htsfile.o libhts.a
tabix: tabix.o libhts.a
$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread

annot-tsv: annot-tsv.o libhts.a
$(CC) $(LDFLAGS) -o $@ annot-tsv.o libhts.a $(LIBS) -lpthread

annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h)
bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)
htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(htslib_hts_log_h)
annot-tsv.o: annot-tsv.c config.h $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_regidx_h)

# Runes to check that the htscodecs submodule is present
ifdef HTSCODECS_SOURCES
Expand Down Expand Up @@ -868,7 +862,7 @@ install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB
if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
$(INSTALL_DATA) $(SRC)htslib/*.h $(DESTDIR)$(includedir)/htslib
$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
$(INSTALL_MAN) $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir)
$(INSTALL_MAN) $(SRC)annot-tsv.1 $(SRC)bgzip.1 $(SRC)htsfile.1 $(SRC)tabix.1 $(DESTDIR)$(man1dir)
$(INSTALL_MAN) $(SRC)faidx.5 $(SRC)sam.5 $(SRC)vcf.5 $(DESTDIR)$(man5dir)
$(INSTALL_MAN) $(SRC)htslib-s3-plugin.7 $(DESTDIR)$(man7dir)

Expand Down
1 change: 0 additions & 1 deletion config.mk.in
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Expand Up @@ -118,4 +118,3 @@ endif
HTS_CFLAGS_AVX2 = @hts_cflags_avx2@
HTS_CFLAGS_AVX512 = @hts_cflags_avx512@
HTS_CFLAGS_SSE4 = @hts_cflags_sse4@
HTS_HAVE_NEON = @hts_have_neon@
7 changes: 4 additions & 3 deletions cram/cram_index.c
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Original file line number Diff line number Diff line change
Expand Up @@ -737,10 +737,11 @@ int cram_index_container(cram_fd *fd,
int ret;

spos = htell(fd->fp);
if (spos - cpos - c->offset != c->landmark[j]) {
if (spos - cpos - (off_t) c->offset != c->landmark[j]) {
hts_log_error("CRAM slice offset %"PRId64" does not match"
" landmark %d in container header (%d)",
spos - cpos - c->offset, j, c->landmark[j]);
" landmark %d in container header (%"PRId32")",
(int64_t) (spos - cpos - (off_t) c->offset),
j, c->landmark[j]);
return -1;
}

Expand Down
12 changes: 7 additions & 5 deletions htslib/sam.h
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Expand Up @@ -2216,7 +2216,7 @@ int sam_prob_realn(bam1_t *b, const char *ref, hts_pos_t ref_len, int flag);
@field canonical_base The canonical base referred to in the MM tag.
One of A, C, G, T or N. Note this may not be the
explicit base recorded in the SEQ column (esp. if N).
@field stran 0 or 1, indicating + or - strand from MM tag.
@field strand 0 or 1, indicating + or - strand from MM tag.
@field qual Quality code (256*probability), or -1 if unknown

@discussion
Expand All @@ -2230,10 +2230,10 @@ typedef struct hts_base_mod {
int qual;
} hts_base_mod;

#define HTS_MOD_UNKNOWN -1 // In MM but no ML
#define HTS_MOD_UNKNOWN -1 // In MM but not ML
#define HTS_MOD_UNCHECKED -2 // Not in MM and in explicit mode

// Flags for hts_parse_basemod2
// Flags for bam_parse_basemod2
#define HTS_MOD_REPORT_UNCHECKED 1

/// Allocates an hts_base_mode_state.
Expand All @@ -2259,7 +2259,7 @@ hts_base_mod_state *hts_base_mod_state_alloc(void);
HTSLIB_EXPORT
void hts_base_mod_state_free(hts_base_mod_state *state);

/// Parses the Mm and Ml tags out of a bam record.
/// Parses the MM and ML tags out of a bam record.
/**
* @param b BAM alignment record
* @param state The base modification state pointer.
Expand All @@ -2268,11 +2268,12 @@ void hts_base_mod_state_free(hts_base_mod_state *state);
*
* This fills out the contents of the modification state, resetting the
* iterator location to the first sequence base.
* (Parses the draft Mm/Ml tags instead if MM and/or ML are not present.)
*/
HTSLIB_EXPORT
int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state);

/// Parses the Mm and Ml tags out of a bam record.
/// Parses the MM and ML tags out of a bam record.
/**
* @param b BAM alignment record
* @param state The base modification state pointer.
Expand All @@ -2283,6 +2284,7 @@ int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state);
*
* This fills out the contents of the modification state, resetting the
* iterator location to the first sequence base.
* (Parses the draft Mm/Ml tags instead if MM and/or ML are not present.)
*/
HTSLIB_EXPORT
int bam_parse_basemod2(const bam1_t *b, hts_base_mod_state *state,
Expand Down