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Merged
daviesrob merged 3 commits into from
Jun 17, 2026
+4 −4
Merged

Miscellaneous trivia and minor fixes #2035

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7df834c
Use isalpha_c() wrapper
jmarshall May 26, 2026
6b12ae5
Add missing Makefile dependencies [minor]
jmarshall Jun 13, 2026
cfe2223
Don't dereference fp after bgzf_close() may have freed it
jmarshall Jun 15, 2026
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4 changes: 2 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -527,7 +527,7 @@ realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_hts_alloc_h) $(hts
textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(htslib_sam_h) $(hts_internal_h)

cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(fuzz_settings_h) $(htslib_hts_alloc_h) $(htslib_hts_endian_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_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) $(htslib_hts_alloc_h) $(htslib_hfile_h)
cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_alloc_h) $(htslib_hfile_h) $(sam_internal_h)
cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(sam_internal_h) $(htslib_hts_h) $(htslib_hts_alloc_h) $(htslib_hts_endian_h) $(textutils_internal_h)
cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(htslib_hts_alloc_h) $(cram_h)
cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_hts_alloc_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
Expand Down Expand Up @@ -900,7 +900,7 @@ test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_hts_alloc_h) $(htslib_h
test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)
test/test_introspection.o: test/test_introspection.c config.h $(htslib_hts_h) $(htslib_hfile_h)
test/test-bcf_set_variant_type.o: test/test-bcf_set_variant_type.c config.h $(htslib_hts_h) vcf.c
test/test_hfile_libcurl.o: test/test_hfile_libcurl.c config.h $(htslib_hfile_h) $(htslib_hts_h)
test/test_hfile_libcurl.o: test/test_hfile_libcurl.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(hts_internal_h)

# Standalone target not added to $(BUILT_TEST_PROGRAMS) as some may not
# have a compiler that compiles as C++ when given a .cpp source file.
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2 changes: 1 addition & 1 deletion bgzip.c
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Expand Up @@ -515,7 +515,7 @@ int main(int argc, char **argv)

if (!write_fname) {
if (bgzf_close(fp) < 0)
error("Output close failed: Error %d\n", fp->errcode);
error("Output close failed\n");
}

if (hclose(f_src) < 0)
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2 changes: 1 addition & 1 deletion sam.c
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Expand Up @@ -3861,7 +3861,7 @@ int fastq_state_set(samFile *fp, enum hts_fmt_option opt, ...) {
bc = "RX";
int ntags = 0, err = 0;
for (ntags = 0; *bc && ntags < UMI_TAGS; ntags++) {
if (!isalpha(bc[0]) || !isalnum_c(bc[1])) {
if (!isalpha_c(bc[0]) || !isalnum_c(bc[1])) {
err = 1;
break;
}
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