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Defaulting convert_ucsc_contig_names to True for consistency with past behavior #253

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Jul 3, 2024
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Defaulting convert_ucsc_contig_names to True for consistency with past behavior #253

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8 changes: 4 additions & 4 deletions varcode/vcf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def load_vcf(
sort_key=variant_ascending_position_sort_key,
distinct=True,
normalize_contig_names=True,
convert_ucsc_contig_names=None):
convert_ucsc_contig_names=True):
"""
Load reference name and Variant objects from the given VCF filename.

Expand Down Expand Up @@ -98,10 +98,10 @@ def load_vcf(
to uppercase (e.g. "chrx" -> "chrX"). If you don't want
this behavior then pass normalize_contig_names=False.

convert_ucsc_contig_names : bool
convert_ucsc_contig_names : bool, default True
Convert chromosome names from hg19 (e.g. "chr1") to equivalent names
for GRCh37 (e.g. "1"). By default this is set to True if the genome
of the VCF is a UCSC reference and otherwise set to False.
for GRCh37 (e.g. "1"). By default this is set to True. If None, it
also evaluates to True if the genome of the VCF is a UCSC reference.
"""

require_string(path, "Path or URL to VCF")
Expand Down
2 changes: 1 addition & 1 deletion varcode/version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "1.2.0"
__version__ = "1.2.1"
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