VariantDatasetCombiner documentation out of date?

[Maarten-vd-Sande]

What happened?

When running the code example of the VariantDatasetCombiner, I can succesfully execute the combiner.run() code. The last line of the example, is not correct anymore: vds = hl.read_vds('gs://bucket/dataset.vds'). This should I think be turned into a hl.vds.read_vds call.

https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html

** ignore all below, my gvcfs were not correctly formatted!! **

Nevertheless, when I replace it, I get the error:

annotate_globals: keyword argument 'ref_block_max_length': expected expression of type any, found NoneType: None

Not sure if it is related to the fact that I have a non-human genome?

This is the script I run:

intervals = []
interval_size = 10_000_000

# loop over each chromosome and its length
for chrom, length in chrom_lengths.items():
    # create intervals in steps of 10,000,000 bases
    for start in range(1, length + 1, interval_size):
        end = min(start + interval_size - 1, length)
        interval = hl.Interval(
            hl.Locus(chrom, start, reference_genome=dm6_ref),
            hl.Locus(chrom, end, reference_genome=dm6_ref)
        )
        hl.eval(interval)
        intervals.append(interval)

gvcfs = [
    'vcfs/0.g.vcf.gz',
    'vcfs/1.g.vcf.gz',
]

combiner = hl.vds.new_combiner(
    output_path='combined_vcfs.vds',
    temp_path='/tmp',
    gvcf_paths=gvcfs,
    reference_genome=dm6_ref,
    use_exome_default_intervals=False,
    use_genome_default_intervals=False,
    intervals=intervals,
)

combiner.run()  # <-- still works

vds = hl.vds.read_vds(  # <-- doesn't work!
    'combined_vcfs.vds',
)

Not sure if I misunderstand how to work with a non-human reference genome and the intervals?

Version

version 0.2.133-4c60fddb171a

Relevant log output

No response