Hi, I ran into this issue when I am reading vcf file:
ValueError: invalid literal for int() with base 10: '48169282.0': Error while type casting for column 'pos'
Version: snps 2.8.1
OS: MacOS Sonoma 14.3.1 with Apple M1 chip
Here is part of my DNA raw data downloaded from AncestryDNA:
# This data file generated by 23andMe at: Sat Jun 12 11:23:12 2024
#
# This file contains raw genotype data, including data that is not used in 23andMe reports.
#
# Each line corresponds to a single SNP. For each SNP, we provide its identifier (an rsid
# or an internal id), its location on the reference human genome, and the genotype call
# oriented with respect to the plus strand on the reference human genome. We are using reference
# human assembly build 37 (also known as Annotation Release 104).
#
# More information on these variants can be found at http://www.ncbi.nlm.nih.gov/SNP/
#
# rsid chromosome position genotype
rs1 17 21102678 AG
rs2 7 62361768 AA
rs3 18 42763504 CT
...
And here is part of the converted vcf file using to_vcf():
##fileformat=VCFv4.2
##fileDate=20240613
...
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
1 48169282.0 rs112 C A,T . . . GT 2/1
...
Hi, I ran into this issue when I am reading vcf file:
ValueError: invalid literal for int() with base 10: '48169282.0': Error while type casting for column 'pos'
Version: snps 2.8.1 OS: MacOS Sonoma 14.3.1 with Apple M1 chip
Here is part of my DNA raw data downloaded from AncestryDNA:
And here is part of the converted vcf file using
to_vcf()
:As you can see "POS" became float (48169282.0) instead of
np.uint32
as here suggested https://github.com/apriha/snps/blob/master/src/snps/io/reader.pyIf I change "48169282.0" to "48169282" the error would be gone but I didn't know if it is expected data type. Enlightenments are appreciated.
Thank you.