From ddf49e4cce3978368cc08e015e5d1492a5b7c93f Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 16 Jan 2023 11:57:58 +1100 Subject: basic README and license --- LICENSE | 19 +++++++++++++++++++ README | 5 +++++ package.yaml | 3 +-- phylogenies.cabal | 4 ++-- 4 files changed, 27 insertions(+), 4 deletions(-) create mode 100644 LICENSE create mode 100644 README diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..b31a8ce --- /dev/null +++ b/LICENSE @@ -0,0 +1,19 @@ +Copyright (c) 2022–2023 Justin Bedő + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README b/README new file mode 100644 index 0000000..e9503bc --- /dev/null +++ b/README @@ -0,0 +1,5 @@ +This infers a phylogentic tree from SNV calls. The input file format is textual +with rows corresponding to (copy-neutral) SNV calls that contain an identifier +(ignored) and any number count/depth pairs separated by whitespace. Count and +depth must be natural numbers with count ≤ depth. See `--help` flag for +options. diff --git a/package.yaml b/package.yaml index 8290eed..23b8f71 100644 --- a/package.yaml +++ b/package.yaml @@ -1,6 +1,6 @@ name: phylogenies version: 0.0.1 -synopsis: phylogeny playground +synopsis: phylogeny inferencing maintainer: Justin Bedo license: MIT @@ -13,6 +13,5 @@ executable: - ppl - containers - log-domain - - vector - random - optparse-applicative diff --git a/phylogenies.cabal b/phylogenies.cabal index e8cea10..3702eaa 100644 --- a/phylogenies.cabal +++ b/phylogenies.cabal @@ -6,9 +6,10 @@ cabal-version: 1.12 name: phylogenies version: 0.0.1 -synopsis: phylogeny playground +synopsis: phylogeny inferencing maintainer: Justin Bedo license: MIT +license-file: LICENSE build-type: Simple executable phylogenies @@ -25,5 +26,4 @@ executable phylogenies , optparse-applicative , ppl , random - , vector default-language: Haskell2010 -- cgit v1.2.3