diff --git a/varcode/vcf.py b/varcode/vcf.py index f4ca45d..1c25ba8 100644 --- a/varcode/vcf.py +++ b/varcode/vcf.py @@ -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. @@ -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") diff --git a/varcode/version.py b/varcode/version.py index c68196d..a955fda 100644 --- a/varcode/version.py +++ b/varcode/version.py @@ -1 +1 @@ -__version__ = "1.2.0" +__version__ = "1.2.1"