Issues

• Add option to disable partially-mapped reads filter on align command

  backburnerenhancementgood first issue
  fedarko/strainFlye#71 · Filter by author fedarko opened on Sep 24, 2024

• Bizarre mamba installation error for a python 3.7.16 environment

  buginstallation
  fedarko/strainFlye#70 · Filter by author fedarko opened on Sep 14, 2023
  1

• Reject contigs with names that would break bcftools

  buggood first issue
  fedarko/strainFlye#65 · Filter by author fedarko opened on Jan 26, 2023

• Use pyfaidx to access contigs in FASTA files

  performance
  fedarko/strainFlye#64 · Filter by author fedarko opened on Nov 7, 2022

• Output un-normalized coverages from "dynam covskew"

  documentationenhancement
  fedarko/strainFlye#63 · Filter by author fedarko opened on Nov 3, 2022

• More efficient contig subsetting

  enhancementperformance
  fedarko/strainFlye#62 · Filter by author fedarko opened on Oct 29, 2022

• Fix CI warnings from GitHub Actions

  administrativetesting
  fedarko/strainFlye#61 · Filter by author fedarko opened on Oct 25, 2022

• Consistent behavior on delaying creation of the output file(s) / output directory

  backburner
  fedarko/strainFlye#60 · Filter by author fedarko opened on Oct 21, 2022

• Close BAM files after every command / test that loads them

  backburnerquestion
  fedarko/strainFlye#59 · Filter by author fedarko opened on Oct 19, 2022

• Combining downstream commands

  future ideasperformance
  fedarko/strainFlye#58 · Filter by author fedarko opened on Oct 15, 2022

• Ensure that contig names can be used within filenames

  backburnerbug
  fedarko/strainFlye#57 · Filter by author fedarko opened on Oct 13, 2022

• Including (some) rare mutations from the decoy contig in the "fdr fix" BCF?

  backburnerenhancementfuture ideas
  fedarko/strainFlye#54 · Filter by author fedarko opened on Sep 30, 2022

• Compress TSV outputs?

  backburnerperformance
  fedarko/strainFlye#53 · Filter by author fedarko opened on Sep 23, 2022

• Replace lists of numbers used for diversity index p / r values with multiple=True?

  backburner
  fedarko/strainFlye#51 · Filter by author fedarko opened on Sep 21, 2022

• Output file of "unreasonable position" information during naive calling

  enhancementperformance
  fedarko/strainFlye#48 · Filter by author fedarko opened on Sep 11, 2022

• Smoothed read creation: only (re-)compute average coverages for contigs with > 0 mutations

  performance
  fedarko/strainFlye#44 · Filter by author fedarko opened on Aug 27, 2022

• Speed up input BCF validation

  performance
  fedarko/strainFlye#43 · Filter by author fedarko opened on Aug 25, 2022

• Warn / fail when we encounter massive datasets?

  documentationnotestesting
  fedarko/strainFlye#37 · Filter by author fedarko opened on Aug 19, 2022

• Parallelizing certain operations

  future ideasperformance
  fedarko/strainFlye#36 · Filter by author fedarko opened on Aug 18, 2022

• Warn user if an input BCF contains no mutations across any contigs

  enhancementtesting
  fedarko/strainFlye#35 · Filter by author fedarko opened on Aug 17, 2022

• Notes on overwriting

  documentationnotestesting
  fedarko/strainFlye#34 · Filter by author fedarko opened on Aug 17, 2022

• Support circular GFF3 features in hotspot detection?

  backburner
  fedarko/strainFlye#31 · Filter by author fedarko opened on Aug 11, 2022

• Additional minimap2 parameters that are useful for HiFi data

  backburnerenhancement
  fedarko/strainFlye#29 · Filter by author fedarko opened on Jun 14, 2022

• Generalize to multi-allelic mutations

  future ideas
  fedarko/strainFlye#28 · Filter by author fedarko opened on Jun 13, 2022

• Clearer explanation of "rare" / indisputable mutations in the tutorial?

  documentation
  fedarko/strainFlye#27 · Filter by author fedarko opened on Jun 6, 2022