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Fix coverage summary #126
Fix coverage summary #126
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@jmtsuji This sounds good. Feel free to create an issue for this. |
Will include in issue #120 |
@jmtsuji Looks good to me at a glance. Feel free to merge in. |
Fixes a couple intertwined issues in rule
summarize_contigs_by_coverage
that caused errors when running rotary in long read only mode, to address one part of #118In the previous version of rotary, long-read only mode actually worked with rule
summarize_contigs_by_coverage
, but only when a coverage filter threshold was supplied in the config file. The rule resulted in an error when no long read coverage filter thresholds were supplied (which is the config default) in long-read only mode.In this update, the following changes were made to address this problem:
summarize_contigs_by_coverage
was moved inside a conditional block (as it should have always been) so that it only runs when some kind of coverage filtration is requested{sample}/polish/{sample}_contig_info.tsv
. This report is made whether coverage filtration is performed or not.split_circular_and_linear_contigs
-- before, no report was made if coverage filtration was not run, causing this checkpoint to fail.Because of how rule
summarize_contigs_by_coverage
was moved into an existing conditional block inpolish.smk
, the git diff does not show the file changes very cleanly -- my apologies!In the long term, I think it might make sense to move the code in
summarize_contigs_by_coverage
into a Python utility script -- this would make it easier to write/run tests on some of the logic being performed in this code.Let me know if you have any thoughts -- thanks!