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samtools
bcftools --write-index creates sometimes indexes older than the data file.
bcftools --write-index creates sometimes indexes older than the data file.
# Create BCF files from VCF files and create index on the fly.
for i in $(seq 1 200); do
sample=$(printf '%03d' "$i");
echo ${sample};
bcftools view --threads 2 --write-index -O b -o ${sample}.bcf ${sample}.vcf
done
# Merge all BCF files.
$ bcftools merge --threads 8 -O b --write-index -o merged.bcf *.bcf
[W::hts_idx_load3] The index file is older than the data file: 051.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 107.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 125.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 130.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 134.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 149.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 155.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 160.bcf.csi
[W::hts_idx_load3] The index file is older than the data file: 187.bcf.csi
# Modification times:
$ stat 051.bcf
File: 051.bcf
Size: 51212037 Blocks: 100032 IO Block: 4194304 regular file
Device: 25c66b0ah/633760522d Inode: 144120644294937758 Links: 1
Access: (0644/-rw-r--r--) Uid: (2530366/ghuls) Gid: (2631836/ group)
Access: 2024-01-23 13:20:56.000000000 +0100
Modify: 2024-01-23 10:02:50.000000000 +0100
Change: 2024-01-23 10:02:50.000000000 +0100
Birth: 2024-01-22 17:12:36.000000000 +0100
❯ stat 051.bcf.csi
File: 051.bcf.csi
Size: 1379257 Blocks: 2696 IO Block: 4194304 regular file
Device: 25c66b0ah/633760522d Inode: 144120644294937767 Links: 1
Access: (0644/-rw-r--r--) Uid: (2530366/ghuls) Gid: (2631836/ group)
Access: 2024-01-23 13:19:23.000000000 +0100
Modify: 2024-01-23 10:02:49.000000000 +0100
Change: 2024-01-23 10:02:49.000000000 +0100
Birth: 2024-01-22 17:12:46.000000000 +0100
Could the index be "touched" (so last modification time is updated) after the BCF file is closed?
https://github.com/samtools/bcftools/blob/develop/vcfview.c#L825-L835
