1.0.0 (#62)

* Adjusted the name of the TSV output flag ("--ultra" -> "--tsv"

* Adjusted the default memory window sizing algorithm.

* Adjusting example fasta files.

* Adjusting example fasta files.

* Fixed an repeat splitting output bug in TabFileWriter

* Removing json11 lib files, adjusting default tuning parameters, fixing bugs with --fdr

* Including a new example fasta

* Adjusting JSOn output and ULTRA TSV output extension (.ultra -> .tsv)

* Improving README and adding in an example tune_file.

* Update README.md

Fixing README typos

* Update README.md

README wordsmithing

* Update README.md

Typo fix in example 2 of the README

* Update README.md

More improvements to example 2

* Update README.md

Improvements to example 3

* Update README.md

More improvements to example 3

* Update README.md

Improvements to the output format section

* Update README.md

Improvements to json format section of tuning guide

* Added a --cite flag

* Adding a workflow for building/storing binaries.

Author: DanielOlson

.github/workflows/build.yml

@@ -0,0 +1,43 @@
+name: Build and Release
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'  # Trigger only on version tags
+  pull_request:
+    tags:
+      - 'v*.*.*'  # Trigger only on version tags
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up CMake
+        uses: lukka/get-cmake@v3
+
+      - name: Install dependencies
+        run: sudo apt-get update && sudo apt-get install -y build-essential
+
+      - name: Configure CMake
+        run: cmake -S . -B build
+
+      - name: Build with CMake
+        run: cmake --build build --config Release
+
+      - name: Create zip archive of binaries
+        run: |
+          mkdir build_output
+          cp build/ultra build_output/
+          zip -r binaries_${{ github.ref_name }}.zip build_output/
+        shell: bash
+
+      - name: Upload binaries to GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: binaries_${{ github.ref_name }}.zip
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CMakeLists.txt

@@ -16,8 +16,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set(
         LIB_CPP_FILES
-
-        lib/json11.cpp
 )
 set(
         HPP_FILES
@@ -57,7 +55,8 @@ set(
         src/JSONFileWriter.cpp
         src/RepeatSplitter.cpp
         src/mask.cpp
-        src/cli.cpp src/TabFileWriter.hpp)
+        src/cli.cpp
+        )
 
 find_package(Threads REQUIRED)