You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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 suggestedhttps://github.com/apriha/snps/blob/master/src/snps/io/reader.py
If 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.
The text was updated successfully, but these errors were encountered: