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Add option to disable partially-mapped reads filter on align command
backburnerLow-priority things that are still good to keep track ofLow-priority things that are still good to keep track ofenhancementNew feature or requestNew feature or requestgood first issueGood for newcomersGood for newcomersStatus: Open.#71 In fedarko/strainFlye;Bizarre mamba installation error for a python 3.7.16 environment
bugSomething isn't workingSomething isn't workinginstallationEverybody's favorite part of bioinformaticsEverybody's favorite part of bioinformaticsStatus: Open.#70 In fedarko/strainFlye;Reject contigs with names that would break bcftools
bugSomething isn't workingSomething isn't workinggood first issueGood for newcomersGood for newcomersStatus: Open.#65 In fedarko/strainFlye;- Status: Open.#64 In fedarko/strainFlye;
Output un-normalized coverages from "dynam covskew"
documentationImprovements or additions to documentationImprovements or additions to documentationenhancementNew feature or requestNew feature or requestStatus: Open.#63 In fedarko/strainFlye;More efficient contig subsetting
enhancementNew feature or requestNew feature or requestperformancegotta go fastgotta go fastStatus: Open.#62 In fedarko/strainFlye;Fix CI warnings from GitHub Actions
administrativeLogistical, non-code-related thingsLogistical, non-code-related thingstestingPlans for future tests, issues with current tests, etc.Plans for future tests, issues with current tests, etc.Status: Open.#61 In fedarko/strainFlye;Consistent behavior on delaying creation of the output file(s) / output directory
backburnerLow-priority things that are still good to keep track ofLow-priority things that are still good to keep track ofStatus: Open.#60 In fedarko/strainFlye;Close BAM files after every command / test that loads them
backburnerLow-priority things that are still good to keep track ofLow-priority things that are still good to keep track ofquestionFurther information is requestedFurther information is requestedStatus: Open.#59 In fedarko/strainFlye;Combining downstream commands
future ideaslonger-term enhancements that'd require a lot of extra time/attentionlonger-term enhancements that'd require a lot of extra time/attentionperformancegotta go fastgotta go fastStatus: Open.#58 In fedarko/strainFlye;Ensure that contig names can be used within filenames
backburnerLow-priority things that are still good to keep track ofLow-priority things that are still good to keep track ofbugSomething isn't workingSomething isn't workingStatus: Open.#57 In fedarko/strainFlye;Including (some) rare mutations from the decoy contig in the "fdr fix" BCF?
backburnerLow-priority things that are still good to keep track ofLow-priority things that are still good to keep track ofenhancementNew feature or requestNew feature or requestfuture ideaslonger-term enhancements that'd require a lot of extra time/attentionlonger-term enhancements that'd require a lot of extra time/attentionStatus: Open.#54 In fedarko/strainFlye;