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campanam / RatesTools

Pipeline to calculate de novo mutation rates from parent-offspring trios
Creative Commons Zero v1.0 Universal
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[FEATURE REQUEST] option to turn off region filter #51

Closed campanam closed 11 months ago

campanam commented 2 years ago

Feature request description
Might be helpful to be able to turn off region filter. Process still needs to convert bgzipped file to gzip for calc_denovo_mutation_rate.rb

campanam commented 2 years ago

This will require additional coding of dnm_summary_stats as the script crashes with the region filters disabled.

campanam commented 2 years ago

/home/campanam/bin/dnm_summary_stats.rb:69:in block in classify_sites': undefined method+' for nil:NilClass (NoMethodError) from /home/campanam/bin/dnm_summary_stats.rb:48:in open' from /home/campanam/bin/dnm_summary_stats.rb:48:inclassify_sites' from /home/campanam/bin/dnm_summary_stats.rb:145:in block in <main>' from /home/campanam/bin/dnm_summary_stats.rb:144:ineach' from /home/campanam/bin/dnm_summary_stats.rb:144:in `

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campanam commented 11 months ago

Added in DSL2 version and updates completed