From b2584fb7c17bef46fc9fa0d478a577fe188f97c2 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Sat, 13 Jun 2026 21:17:29 +1200 Subject: [PATCH 1/3] Allow for clock() returning floating point [minor] POSIX allows clock_t to be either an integer or a real-floating type, but ^ requires integers. Signed-off-by: John Marshall --- bcftools.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bcftools.h b/bcftools.h index e31caa00..53ae81a9 100644 --- a/bcftools.h +++ b/bcftools.h @@ -82,7 +82,7 @@ int parse_overlap_option(const char *arg); // make random seed which safe for parallelization static inline uint32_t make_seed(void) { - return (uint32_t)(time(NULL) ^ (getpid() << 16) ^ clock()); + return (uint32_t)(time(NULL) ^ (getpid() << 16) ^ (uint32_t) clock()); } // Default sort order: chr,pos,alleles From 4f4fb20c16a417499eb694aef25a719ad2716c15 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Sun, 14 Jun 2026 21:22:04 +1200 Subject: [PATCH 2/3] Fix Makefile dependencies [minor] Signed-off-by: John Marshall --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 72153f9f..9bbde007 100644 --- a/Makefile +++ b/Makefile @@ -254,7 +254,7 @@ vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(hts vcfplugin.o: vcfplugin.c config.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) vcfcall.o: vcfcall.c $(htslib_vcf_h) $(htslib_kfunc_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h) $(gvcf_h) regidx.h $(vcfbuf_h) vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) $(bcftools_h) -vcfconvert.o: vcfconvert.c $(htslib_faidx_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kseq_h) $(htslib_hts_endian_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) +vcfconvert.o: vcfconvert.c $(htslib_faidx_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kseq_h) $(htslib_hts_endian_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h) $(vcfbuf_h) vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h regidx.h vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(htslib_hts_os_h) $(htslib_bgzf_h) $(bcftools_h) extsort.h $(filter_h) vcfindex.o: vcfindex.c $(htslib_vcf_h) $(htslib_tbx_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(bcftools_h) @@ -300,7 +300,7 @@ read_consensus.o: read_consensus.c $(read_consensus_h) $(cigar_state_h) $(bcftoo bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h) version.o: version.c $(htslib_hts_h) $(bcftools_h) version.h hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h -HMM.o: HMM.c $(htslib_hts_h) HMM.h +HMM.o: HMM.c HMM.h vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(htslib_kbitset_h) $(bcftools_h) $(vcfbuf_h) rbuf.h abuf.o: abuf.c $(htslib_vcf_h) $(bcftools_h) rbuf.h abuf.h edlib.o: edlib.c edlib.h From a006b1af44f0e763a22b90ab1afb5d12987a2219 Mon Sep 17 00:00:00 2001 From: John Marshall Date: Sun, 14 Jun 2026 21:37:12 +1200 Subject: [PATCH 3/3] Fix trivial typo [minor] Signed-off-by: John Marshall --- mpileup.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mpileup.c b/mpileup.c index 781dd4fa..29c6717c 100644 --- a/mpileup.c +++ b/mpileup.c @@ -294,7 +294,7 @@ static int mplp_func(void *data, bam1_t *b) else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue; return ret; - }; + } return ret; }