rebin does not generate the correct number of bins

[js2264]

• Generating cools with hicstuff rebin or cooler cload

conda activate hicstuff
hicstuff pipeline --enzyme "DpnII,HinfI" --mapping normal --prefix "test" --outdir "results" --threads 4 --genome ~/genomes/S288c/S288c.fa test_R1.fq test_R2.fq
hicstuff rebin --binning 1kb --frags results/test.frags.tsv --chroms results/test.chr.tsv results/test.cool results/test_rebin
cooler cload pairs --chrom1 2 --pos1 3 --chrom2 4 --pos2 5 <(sed 1d results/test.chr.tsv | cut -f1-2):1000 results/test.valid_idx.pairs results/test_cooler-cload.cool

• Checking nbins

$ cooler info results/test_cooler-cload.cool
{
    "bin-size": 1000,
    "bin-type": "fixed",
    "creation-date": "2023-09-06T13:09:51.878188",
    "format": "HDF5::Cooler",
    "format-url": "https://github.com/open2c/cooler",
    "format-version": 3,
    "generated-by": "cooler-0.9.2",
    "genome-assembly": "unknown",
    **"nbins": 12165,**
    "nchroms": 17,
    "nnz": 62062,
    "storage-mode": "symmetric-upper",
    "sum": 69118
}
$ cooler info results/test_rebin.cool 
{
    "bin-size": 1000,
    "bin-type": "fixed",
    "creation-date": "2023-09-06T13:10:22.453334",
    "format": "HDF5::Cooler",
    "format-url": "https://github.com/open2c/cooler",
    "format-version": 3,
    "generated-by": "cooler-0.9.2",
    "genome-assembly": "unknown",
    **"nbins": 12157,**
    "nchroms": 17,
    "nnz": 61745,
    "storage-mode": "symmetric-upper",
    "sum": 69118
}

• Checking bins table

$ cooler dump --table bins results/test_cooler-cload.cool | grep -P "XV\t" | tail -n 3
XV      1089000 1090000
**XV      1090000 1091000
XV      1091000 1091291**
$ cooler dump --table bins results/test_rebin.cool | grep -P "XV\t" | tail -n 3
XV      1088000 1089000
**XV      1089000 1090000
XV      1090000 1091291**

• Actual chromosome XVI length

$ cat ~/genomes/S288c/S288c.fa.fai | cut -f1-2 | grep -P "XV\t" 
XV      1091291