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reformat print line to get rid off unwanted spaces

Open WardDeb opened this issue 6 months ago • 2 comments

Hi, Thanks for the software ! I've noticed that the extract_snps script introduces spaces directly after the geno[1] field, at the position where the print line is split up over multiple lines. This causes issues in the assignment later on as no reads can be assigned to the alternative genotype. The pipeline fails later in the matrix generation.

Reformatting this line gets rid of the spaces and fixes the issues downstream.

I've tested with mgp_REL2021_snps.vcf.gz, corresponding to GRCm39.

Related to #572.

Kind regards,

WardDeb

WardDeb avatar Dec 11 '23 12:12 WardDeb