feat: use pybwa

fulcrumgenomics · Jan 17, 2025 · cfed0c0 · cfed0c0
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diff --git a/README.md b/README.md
@@ -47,7 +47,7 @@
 
 ## Recommended Installation
 
-The package `prymer` requires installation of [Primer3](https://github.com/primer3-org/primer3) and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).
+The package `prymer` requires installation of [Primer3](https://github.com/primer3-org/primer3).
 
 To satisfy these requirements, it is recommended to install using [bioconda](https://bioconda.github.io/):
 

diff --git a/docs/installation-and-developers-documentation.md b/docs/installation-and-developers-documentation.md
@@ -14,25 +14,24 @@ mamba install -c bioconda prymer
 
 1. Install the environment manager [`mamba`](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)
 2. Install the Python build tool [`poetry`](https://python-poetry.org/docs/#installing-with-the-official-installer)
-3. Create an environment with Python, [Primer3](https://github.com/primer3-org/primer3), and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive):
 
     ```console
     mamba env create -y -f prymer.yml
     ```
 
-4. Activate the environment:
+3. Activate the environment:
 
     ```console
     mamba activate prymer
     ```
 
-5. Configure `poetry` to install into pre-existing virtual environments:
+4. Configure `poetry` to install into pre-existing virtual environments:
 
     ```console
     poetry config virtualenvs.create false
     ```
 
-6. Install `prymer` into the virtual environment:
+5. Install `prymer` into the virtual environment:
 
     ```console
     poetry install

diff --git a/poetry.lock b/poetry.lock
diff --git a/prymer.yml b/prymer.yml
@@ -3,6 +3,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bioconda::bwa-aln-interactive=0.7.18
   - bioconda::primer3=2.6.1
   - conda-forge::python>=3.11.*
diff --git a/prymer/offtarget/__init__.py b/prymer/offtarget/__init__.py
@@ -1,12 +1,12 @@
-from prymer.offtarget.bwa import BwaAlnInteractive
+from prymer.offtarget.bwa import Bwa
 from prymer.offtarget.bwa import BwaHit
 from prymer.offtarget.bwa import BwaResult
 from prymer.offtarget.bwa import Query
 from prymer.offtarget.offtarget_detector import OffTargetDetector
 from prymer.offtarget.offtarget_detector import OffTargetResult
 
 __all__ = [
-    "BwaAlnInteractive",
+    "Bwa",
     "Query",
     "BwaHit",
     "BwaResult",