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Miscellaneous minor fixes #2568

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Merged
pd3 merged 3 commits into from
Jun 16, 2026
+4 −4
Merged

Miscellaneous minor fixes #2568

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b2584fb
Allow for clock() returning floating point [minor]
jmarshall Jun 13, 2026
4f4fb20
Fix Makefile dependencies [minor]
jmarshall Jun 14, 2026
a006b1a
Fix trivial typo [minor]
jmarshall Jun 14, 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 @@ -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)
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion bcftools.h
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion mpileup.c
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Expand Up @@ -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;
}

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