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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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reformat print line to get rid off unwanted spaces #606

Open WardDeb opened 6 months ago

WardDeb commented 6 months ago

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

nservant commented 5 months ago

Hi @WardDeb Sorry for the delay ... I approved your PR but there is a conflict I do not understand. I'll keep that in mind, and make the modification by hand if necessary. Sorry for that N

WardDeb commented 5 months ago

Thanks @nservant ! and no worries for the delay. I think the conflict came from this line being updated in the devel branch (I forked from master initially). I've resolved the conflict but feel free to move on as you see fit :)

Cheers,

WardDeb