├── .Rbuildignore ├── .gitattributes ├── .github └── workflows │ └── pkgdown.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── import.R ├── microhaplot.R ├── runHaplot.R └── runMicroHap.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── field_selection.png │ ├── index.html │ ├── locus_annotation.png │ ├── main_tab.png │ ├── microhaplot-data-prep.html │ ├── microhaplot-data-prep_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── microhaplot-walkthrough.html │ ├── microhaplot-walkthrough_files │ │ └── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ ├── read_criteria_tab.png │ ├── troubleshoot.html │ └── troubleshoot_files │ │ └── accessible-code-block-0.0.1 │ │ └── empty-anchor.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── index.html │ ├── mvShinyHaplot.html │ ├── prepHaplotFiles.html │ └── runShinyHaplot.html └── sitemap.xml ├── inst ├── extdata │ └── sebastes_sam.tar.gz ├── perl │ ├── fatlib │ │ ├── Algorithm │ │ │ └── C3.pm │ │ ├── B │ │ │ └── Hooks │ │ │ │ ├── EndOfScope.pm │ │ │ │ └── EndOfScope │ │ │ │ ├── PP.pm │ │ │ │ ├── PP │ │ │ │ ├── FieldHash.pm │ │ │ │ └── HintHash.pm │ │ │ │ └── XS.pm │ │ ├── Bio │ │ │ └── Cigar.pm │ │ ├── Class │ │ │ ├── C3.pm │ │ │ └── C3 │ │ │ │ └── next.pm │ │ ├── Devel │ │ │ ├── GlobalDestruction.pm │ │ │ └── TypeTiny │ │ │ │ ├── Perl56Compat.pm │ │ │ │ └── Perl58Compat.pm │ │ ├── Error │ │ │ ├── TypeTiny.pm │ │ │ └── TypeTiny │ │ │ │ ├── Assertion.pm │ │ │ │ ├── Compilation.pm │ │ │ │ └── WrongNumberOfParameters.pm │ │ ├── Eval │ │ │ └── TypeTiny.pm │ │ ├── Exporter │ │ │ ├── Shiny.pm │ │ │ └── Tiny.pm │ │ ├── MRO │ │ │ └── Compat.pm │ │ ├── Method │ │ │ └── Generate │ │ │ │ ├── Accessor.pm │ │ │ │ ├── BuildAll.pm │ │ │ │ ├── Constructor.pm │ │ │ │ └── DemolishAll.pm │ │ ├── Module │ │ │ ├── Implementation.pm │ │ │ └── Runtime.pm │ │ ├── Moo.pm │ │ ├── Moo │ │ │ ├── HandleMoose.pm │ │ │ ├── HandleMoose │ │ │ │ ├── FakeMetaClass.pm │ │ │ │ └── _TypeMap.pm │ │ │ ├── Object.pm │ │ │ ├── Role.pm │ │ │ ├── _Utils.pm │ │ │ ├── _mro.pm │ │ │ ├── _strictures.pm │ │ │ └── sification.pm │ │ ├── Package │ │ │ ├── Stash.pm │ │ │ └── Stash │ │ │ │ ├── Conflicts.pm │ │ │ │ └── PP.pm │ │ ├── Reply │ │ │ └── Plugin │ │ │ │ └── TypeTiny.pm │ │ ├── Sub │ │ │ ├── Defer.pm │ │ │ ├── Exporter │ │ │ │ └── Progressive.pm │ │ │ └── Quote.pm │ │ ├── Test │ │ │ └── TypeTiny.pm │ │ ├── Try │ │ │ └── Tiny.pm │ │ ├── Type │ │ │ ├── Coercion.pm │ │ │ ├── Coercion │ │ │ │ ├── FromMoose.pm │ │ │ │ └── Union.pm │ │ │ ├── Library.pm │ │ │ ├── Params.pm │ │ │ ├── Parser.pm │ │ │ ├── Registry.pm │ │ │ ├── Tiny.pm │ │ │ ├── Tiny │ │ │ │ ├── Class.pm │ │ │ │ ├── Duck.pm │ │ │ │ ├── Enum.pm │ │ │ │ ├── Intersection.pm │ │ │ │ ├── Manual.pod │ │ │ │ ├── Manual │ │ │ │ │ ├── Coercions.pod │ │ │ │ │ ├── Libraries.pod │ │ │ │ │ ├── Optimization.pod │ │ │ │ │ ├── Params.pod │ │ │ │ │ ├── Policies.pod │ │ │ │ │ ├── UsingWithMoo.pod │ │ │ │ │ ├── UsingWithMoose.pod │ │ │ │ │ ├── UsingWithMouse.pod │ │ │ │ │ └── UsingWithOther.pod │ │ │ │ ├── Role.pm │ │ │ │ ├── Union.pm │ │ │ │ └── _HalfOp.pm │ │ │ └── Utils.pm │ │ ├── Types │ │ │ ├── Common │ │ │ │ ├── Numeric.pm │ │ │ │ └── String.pm │ │ │ ├── Standard.pm │ │ │ ├── Standard │ │ │ │ ├── ArrayRef.pm │ │ │ │ ├── Dict.pm │ │ │ │ ├── HashRef.pm │ │ │ │ ├── Map.pm │ │ │ │ ├── ScalarRef.pm │ │ │ │ └── Tuple.pm │ │ │ └── TypeTiny.pm │ │ ├── darwin-thread-multi-2level │ │ │ ├── .meta │ │ │ │ ├── Bio-Cigar-1.01 │ │ │ │ │ ├── MYMETA.json │ │ │ │ │ └── install.json │ │ │ │ ├── Exporter-Tiny-0.042 │ │ │ │ │ ├── MYMETA.json │ │ │ │ │ └── install.json │ │ │ │ └── Type-Tiny-1.000005 │ │ │ │ │ ├── MYMETA.json │ │ │ │ │ └── install.json │ │ │ ├── auto │ │ │ │ ├── Bio │ │ │ │ │ └── Cigar │ │ │ │ │ │ └── .packlist │ │ │ │ ├── Exporter │ │ │ │ │ └── Tiny │ │ │ │ │ │ └── .packlist │ │ │ │ └── Type │ │ │ │ │ └── Tiny │ │ │ │ │ └── .packlist │ │ │ └── perllocal.pod │ │ ├── namespace │ │ │ ├── clean.pm │ │ │ └── clean │ │ │ │ └── _Util.pm │ │ └── oo.pm │ ├── fatpacker.trace │ ├── hapture │ └── hapture.pl └── shiny │ └── microhaplot │ ├── fish1.rds │ ├── fish1_posinfo.rds │ ├── fish2.rds │ ├── fish2_posinfo.rds │ ├── server.R │ └── ui.R ├── man ├── figures │ └── microhaplot-sticker.png ├── mvShinyHaplot.Rd ├── prepHaplotFiles.Rd └── runShinyHaplot.Rd ├── microhaplot.Rproj └── vignettes ├── .gitignore ├── field_selection.png ├── locus_annotation.png ├── main_panel_choice_tabset.png ├── main_tab.png ├── microhaplot-data-prep.Rmd ├── microhaplot-walkthrough.Rmd ├── read_criteria_tab.png └── troubleshoot.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/pkgdown.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/.github/workflows/pkgdown.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/.travis.yml -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/LICENSE.md -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/import.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/R/import.R -------------------------------------------------------------------------------- /R/microhaplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/R/microhaplot.R -------------------------------------------------------------------------------- /R/runHaplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/R/runHaplot.R -------------------------------------------------------------------------------- /R/runMicroHap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/R/runMicroHap.R -------------------------------------------------------------------------------- /README.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/README.Rmd -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/README.md -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/_pkgdown.yml -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/cran-comments.md -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/404.html -------------------------------------------------------------------------------- /docs/LICENSE.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/LICENSE.html -------------------------------------------------------------------------------- /docs/articles/field_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/field_selection.png -------------------------------------------------------------------------------- /docs/articles/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/index.html -------------------------------------------------------------------------------- /docs/articles/locus_annotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/locus_annotation.png -------------------------------------------------------------------------------- /docs/articles/main_tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/main_tab.png -------------------------------------------------------------------------------- /docs/articles/microhaplot-data-prep.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/microhaplot-data-prep.html -------------------------------------------------------------------------------- /docs/articles/microhaplot-data-prep_files/accessible-code-block-0.0.1/empty-anchor.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/microhaplot-data-prep_files/accessible-code-block-0.0.1/empty-anchor.js -------------------------------------------------------------------------------- /docs/articles/microhaplot-walkthrough.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/microhaplot-walkthrough.html -------------------------------------------------------------------------------- /docs/articles/microhaplot-walkthrough_files/accessible-code-block-0.0.1/empty-anchor.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/microhaplot-walkthrough_files/accessible-code-block-0.0.1/empty-anchor.js -------------------------------------------------------------------------------- /docs/articles/read_criteria_tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/read_criteria_tab.png -------------------------------------------------------------------------------- /docs/articles/troubleshoot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/troubleshoot.html -------------------------------------------------------------------------------- /docs/articles/troubleshoot_files/accessible-code-block-0.0.1/empty-anchor.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/articles/troubleshoot_files/accessible-code-block-0.0.1/empty-anchor.js -------------------------------------------------------------------------------- /docs/authors.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/authors.html -------------------------------------------------------------------------------- /docs/bootstrap-toc.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/bootstrap-toc.css -------------------------------------------------------------------------------- /docs/bootstrap-toc.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/bootstrap-toc.js -------------------------------------------------------------------------------- /docs/docsearch.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/docsearch.css -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/docsearch.js -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/link.svg -------------------------------------------------------------------------------- /docs/news/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/news/index.html -------------------------------------------------------------------------------- /docs/pkgdown.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/pkgdown.css -------------------------------------------------------------------------------- /docs/pkgdown.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/pkgdown.js -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/pkgdown.yml -------------------------------------------------------------------------------- /docs/reference/Rplot001.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/reference/Rplot001.png -------------------------------------------------------------------------------- /docs/reference/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/reference/index.html -------------------------------------------------------------------------------- /docs/reference/mvShinyHaplot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/reference/mvShinyHaplot.html -------------------------------------------------------------------------------- /docs/reference/prepHaplotFiles.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/reference/prepHaplotFiles.html -------------------------------------------------------------------------------- /docs/reference/runShinyHaplot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/reference/runShinyHaplot.html -------------------------------------------------------------------------------- /docs/sitemap.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/docs/sitemap.xml -------------------------------------------------------------------------------- /inst/extdata/sebastes_sam.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/extdata/sebastes_sam.tar.gz -------------------------------------------------------------------------------- /inst/perl/fatlib/Algorithm/C3.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Algorithm/C3.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/B/Hooks/EndOfScope.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/B/Hooks/EndOfScope.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/B/Hooks/EndOfScope/PP.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/B/Hooks/EndOfScope/PP.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/B/Hooks/EndOfScope/PP/FieldHash.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/B/Hooks/EndOfScope/PP/FieldHash.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/B/Hooks/EndOfScope/PP/HintHash.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/B/Hooks/EndOfScope/PP/HintHash.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/B/Hooks/EndOfScope/XS.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/B/Hooks/EndOfScope/XS.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Bio/Cigar.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Bio/Cigar.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Class/C3.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Class/C3.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Class/C3/next.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Class/C3/next.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Devel/GlobalDestruction.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Devel/GlobalDestruction.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Devel/TypeTiny/Perl56Compat.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Devel/TypeTiny/Perl56Compat.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Devel/TypeTiny/Perl58Compat.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Devel/TypeTiny/Perl58Compat.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Error/TypeTiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Error/TypeTiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Error/TypeTiny/Assertion.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Error/TypeTiny/Assertion.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Error/TypeTiny/Compilation.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Error/TypeTiny/Compilation.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Error/TypeTiny/WrongNumberOfParameters.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Error/TypeTiny/WrongNumberOfParameters.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Eval/TypeTiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Eval/TypeTiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Exporter/Shiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Exporter/Shiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Exporter/Tiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Exporter/Tiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/MRO/Compat.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/MRO/Compat.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Method/Generate/Accessor.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Method/Generate/Accessor.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Method/Generate/BuildAll.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Method/Generate/BuildAll.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Method/Generate/Constructor.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Method/Generate/Constructor.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Method/Generate/DemolishAll.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Method/Generate/DemolishAll.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Module/Implementation.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Module/Implementation.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Module/Runtime.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Module/Runtime.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/HandleMoose.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/HandleMoose.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/HandleMoose/FakeMetaClass.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/HandleMoose/FakeMetaClass.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/HandleMoose/_TypeMap.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/HandleMoose/_TypeMap.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/Object.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/Object.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/Role.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/Role.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/_Utils.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/_Utils.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/_mro.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/_mro.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/_strictures.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/_strictures.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Moo/sification.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Moo/sification.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Package/Stash.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Package/Stash.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Package/Stash/Conflicts.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Package/Stash/Conflicts.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Package/Stash/PP.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Package/Stash/PP.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Reply/Plugin/TypeTiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Reply/Plugin/TypeTiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Sub/Defer.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Sub/Defer.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Sub/Exporter/Progressive.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Sub/Exporter/Progressive.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Sub/Quote.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Sub/Quote.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Test/TypeTiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Test/TypeTiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Try/Tiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Try/Tiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Coercion.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Coercion.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Coercion/FromMoose.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Coercion/FromMoose.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Coercion/Union.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Coercion/Union.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Library.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Library.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Params.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Params.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Parser.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Parser.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Registry.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Registry.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Class.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Class.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Duck.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Duck.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Enum.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Enum.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Intersection.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Intersection.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/Coercions.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/Coercions.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/Libraries.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/Libraries.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/Optimization.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/Optimization.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/Params.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/Params.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/Policies.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/Policies.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/UsingWithMoo.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/UsingWithMoo.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/UsingWithMoose.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/UsingWithMoose.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/UsingWithMouse.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/UsingWithMouse.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Manual/UsingWithOther.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Manual/UsingWithOther.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Role.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Role.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/Union.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/Union.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Tiny/_HalfOp.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Tiny/_HalfOp.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Type/Utils.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Type/Utils.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Common/Numeric.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Common/Numeric.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Common/String.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Common/String.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/ArrayRef.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/ArrayRef.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/Dict.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/Dict.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/HashRef.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/HashRef.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/Map.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/Map.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/ScalarRef.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/ScalarRef.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/Standard/Tuple.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/Standard/Tuple.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/Types/TypeTiny.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/Types/TypeTiny.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Bio-Cigar-1.01/MYMETA.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Bio-Cigar-1.01/MYMETA.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Bio-Cigar-1.01/install.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Bio-Cigar-1.01/install.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Exporter-Tiny-0.042/MYMETA.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Exporter-Tiny-0.042/MYMETA.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Exporter-Tiny-0.042/install.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Exporter-Tiny-0.042/install.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Type-Tiny-1.000005/MYMETA.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Type-Tiny-1.000005/MYMETA.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/.meta/Type-Tiny-1.000005/install.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/.meta/Type-Tiny-1.000005/install.json -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/auto/Bio/Cigar/.packlist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/auto/Bio/Cigar/.packlist -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/auto/Exporter/Tiny/.packlist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/auto/Exporter/Tiny/.packlist -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/auto/Type/Tiny/.packlist: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/auto/Type/Tiny/.packlist -------------------------------------------------------------------------------- /inst/perl/fatlib/darwin-thread-multi-2level/perllocal.pod: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/darwin-thread-multi-2level/perllocal.pod -------------------------------------------------------------------------------- /inst/perl/fatlib/namespace/clean.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/namespace/clean.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/namespace/clean/_Util.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/namespace/clean/_Util.pm -------------------------------------------------------------------------------- /inst/perl/fatlib/oo.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatlib/oo.pm -------------------------------------------------------------------------------- /inst/perl/fatpacker.trace: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/fatpacker.trace -------------------------------------------------------------------------------- /inst/perl/hapture: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/hapture -------------------------------------------------------------------------------- /inst/perl/hapture.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/perl/hapture.pl -------------------------------------------------------------------------------- /inst/shiny/microhaplot/fish1.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/fish1.rds -------------------------------------------------------------------------------- /inst/shiny/microhaplot/fish1_posinfo.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/fish1_posinfo.rds -------------------------------------------------------------------------------- /inst/shiny/microhaplot/fish2.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/fish2.rds -------------------------------------------------------------------------------- /inst/shiny/microhaplot/fish2_posinfo.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/fish2_posinfo.rds -------------------------------------------------------------------------------- /inst/shiny/microhaplot/server.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/server.R -------------------------------------------------------------------------------- /inst/shiny/microhaplot/ui.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/inst/shiny/microhaplot/ui.R -------------------------------------------------------------------------------- /man/figures/microhaplot-sticker.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/man/figures/microhaplot-sticker.png -------------------------------------------------------------------------------- /man/mvShinyHaplot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/man/mvShinyHaplot.Rd -------------------------------------------------------------------------------- /man/prepHaplotFiles.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/man/prepHaplotFiles.Rd -------------------------------------------------------------------------------- /man/runShinyHaplot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/man/runShinyHaplot.Rd -------------------------------------------------------------------------------- /microhaplot.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/microhaplot.Rproj -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/.gitignore -------------------------------------------------------------------------------- /vignettes/field_selection.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/field_selection.png -------------------------------------------------------------------------------- /vignettes/locus_annotation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/locus_annotation.png -------------------------------------------------------------------------------- /vignettes/main_panel_choice_tabset.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/main_panel_choice_tabset.png -------------------------------------------------------------------------------- /vignettes/main_tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/main_tab.png -------------------------------------------------------------------------------- /vignettes/microhaplot-data-prep.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/microhaplot-data-prep.Rmd -------------------------------------------------------------------------------- /vignettes/microhaplot-walkthrough.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/microhaplot-walkthrough.Rmd -------------------------------------------------------------------------------- /vignettes/read_criteria_tab.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/read_criteria_tab.png -------------------------------------------------------------------------------- /vignettes/troubleshoot.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ngthomas/microhaplot/HEAD/vignettes/troubleshoot.Rmd --------------------------------------------------------------------------------