ShawHahnLab/chiimp

Issues

• Parsing ambiguity in primers & complex STR motifs?

  #103 opened 9 months ago by jmmccar
  2

• Error in `[.data.frame`(obj, , cols_id, drop = FALSE) : undefined columns selected

  #102 opened a year ago by Sven-Winter
  1

• Support IUPAC ambiguity codes in primer sequences

  #40 opened 2 years ago by ressy
  1

• Include adapter trimming and optional primer removal

  #37 opened 2 years ago by ressy
  0

• load_dataset duplicate check should use make_entry_id helper

  #96 opened 2 years ago by ressy
  0

• Tests using png("/dev/null") fail with bitmapType quartz

  #94 opened 2 years ago by ressy
  0

• Warnings should be shown closer to where they occurred

  #89 opened 2 years ago by ressy
  0

• load_dataset should complain about overlapping sample+locus+replicate combinations

  #87 opened 2 years ago by ressy
  0

• load_config should check for names not present in config.default

  #58 opened 2 years ago by ressy
  0

• Field order vector for prepare_dataset should optionally be text

  #23 opened 2 years ago by ressy
  1

• CHIIMP.desktop on Linux should have file name field code

  #84 opened 2 years ago by ressy
  0

• Report fails with known genotypes supplied (tabulate_allele_names fails when given exactly one extra column)

  #82 opened 3 years ago by ressy
  0

• Row ordering inconsistent for wide-format genotype summary tables with incomplete sample/locus combinations

  #80 opened 3 years ago by ressy
  0

• Labeling for untested sample/locus combinations is applied to non-locus table columns

  #78 opened 3 years ago by ressy
  0

• Defining sample analysis options per-locus should be available

  #77 opened 3 years ago by ressy
  0

• sample_analysis_opts fraction.min is confusing

  #59 opened 3 years ago by ressy
  0

• Report rendering fails with RStudio >= 2022.02 due to pandoc change

  #73 opened 3 years ago by ressy
  3

• Sample summaries show zero CountTotal when no reads match locus

  #25 opened 6 years ago by ressy
  0

• load_csv should accept row.names if given

  #70 opened 3 years ago by ressy
  0

• Installer commands should obey site-wide configuration

  #71 opened 3 years ago by ressy
  0

• Add interactive tables in reports

  #26 opened 6 years ago by ressy
  0

• Report rendered with pandoc>=2.6 has quotes around title, author, and date

  #68 opened 3 years ago by ressy
  3

• Histogram rendering doesn't handle missing data gracefully

  #65 opened 3 years ago by ressy
  0

• Install should check for for cmd-line dev tools on Mac OS

  #54 opened 5 years ago by ressy
  0

• Migrate from Travis CI for automated testing

  #57 opened 3 years ago by ressy
  0

• plot_dist_mat doesn't handle pheatmap arguments correctly

  #61 opened 3 years ago by ressy
  0

• save_csv should handle missing directories

  #53 opened 3 years ago by ressy
  0

• Desktop icon has incorrect script path on Mac OS

  #55 opened 5 years ago by ressy
  2

• CSV helpers should handle arbitrary columns

  #51 opened 5 years ago by ressy
  0

• Mac OS installer should build .app automatically

  #34 opened 5 years ago by ressy
  0

• Standard reinstall breaks Desktop icon on Mac OS

  #24 opened 5 years ago by ressy
  0

• Reverse primer should be available for use in locus-matching

  #42 opened 5 years ago by ressy
  0

• Stutter/Artifact read count ratio should be configurable

  #41 opened 5 years ago by ressy
  0

• User guide should mention icon usage early on

  #36 opened 5 years ago by ressy
  0

• Desktop icons should give better message when opened directly

  #33 opened 5 years ago by ressy
  1

• Desktop icon needs to be marked as trusted on Ubuntu

  #35 opened 5 years ago by ressy
  1

• CSV input/output should be unified under one function pair

  #39 opened 5 years ago by ressy
  0

• Reorganize installers

  #18 opened 6 years ago by ressy
  3

• Add examples to R package docs for public functions

  #19 opened 6 years ago by ressy
  1

• Spurious test failure during Windows install

  #16 opened 6 years ago by ressy
  2

• Reinstall on Windows fails with broken glue package

  #29 opened 6 years ago by ressy
  1

• R CMD check fails with R-devel_2019-03-11

  #27 opened 6 years ago by ressy
  3

• prepare_dataset gives unintuitive error if data directory missing

  #20 opened 6 years ago by ressy
  1

• tally_cts_per_locus fails if loci are missing in locus attributes table

  #21 opened 6 years ago by ressy
  1

• Heatmap plotting fails when attribute has blanks and a single unique value

  #22 opened 6 years ago by ressy
  1

• Link to demo files in README

  #17 opened 6 years ago by ressy
  1

• Windows install fails if username has spaces

  #11 opened 6 years ago by ressy
  1

• Mac install script should be executable

  #13 opened 6 years ago by ressy
  0

• Tidy release prep utility

  #14 opened 6 years ago by ressy
  0

• save_seqfile_data fails with Windows paths

  #12 opened 6 years ago by ressy
  1