Merge branch 'master' into writing_joss_paper

Author: stschiff

.github/workflows/Dockerfile.centos

@@ -4,9 +4,9 @@ RUN yum -y update
 RUN yum -y install zlib-devel wget ncurses-devel ncurses-compat-libs make gcc gcc-c++
 
 # Install GHC since stack's local install has issues
-RUN wget https://downloads.haskell.org/~ghc/9.4.7/ghc-9.4.7-x86_64-centos7-linux.tar.xz
-RUN tar xvf ghc-9.4.7-x86_64-centos7-linux.tar.xz
-RUN cd ghc-9.4.7-x86_64-unknown-linux; ./configure; make install
+RUN wget https://downloads.haskell.org/~ghc/9.6.6/ghc-9.6.6-x86_64-centos7-linux.tar.xz
+RUN tar xvf ghc-9.6.6-x86_64-centos7-linux.tar.xz
+RUN cd ghc-9.6.6-x86_64-unknown-linux; ./configure; make install
 
 # install stack
 RUN curl -sSL https://get.haskellstack.org/ | sh

.github/workflows/release.yaml

@@ -5,6 +5,7 @@ on:
   push:
     tags:
       - "v*"
+  workflow_dispatch:
 
 jobs:
   create_release:
@@ -27,7 +28,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macOS-13, macOS-14, windows-latest]
+        os: [ubuntu-latest, ubuntu-latest-arm, macOS-13, macOS-latest, windows-latest]
 
     steps:
       - name: Check out code
@@ -56,22 +57,14 @@ jobs:
         run: |
              if [ "$RUNNER_OS" == "Windows" ]; then
                  newEXE="pileupCaller-$RUNNER_OS.exe"
-             elif [ "$RUNNER_OS" == "macOS" ]; then
-                 newEXE="pileupCaller-$RUNNER_OS-$RUNNER_ARCH"
              else
-                 newEXE="pileupCaller-$RUNNER_OS"
+                 newEXE="pileupCaller-$RUNNER_OS-$RUNNER_ARCH"
              fi
              currentEXE="${{ steps.stack.outputs.local-bin }}/pileupCaller"
              mv $currentEXE $newEXE
              echo "BINARY_PATH=$newEXE" >> $GITHUB_OUTPUT
         shell: bash
 
-      - name: Compress binary
-        if: ${{ runner.os != 'macOS' }} # upx is crashing for macOS Ventura or above!
-        uses: svenstaro/upx-action@v2
-        with:
-          files: ${{ steps.binarypath.outputs.BINARY_PATH }}
-
       - name: Upload Release Asset
         id: upload-release-asset
         uses: ncipollo/release-action@v1
@@ -83,30 +76,30 @@ jobs:
           artifacts: ${{ steps.binarypath.outputs.BINARY_PATH }}
           artifactContentType: application/octet-stream
 
-  build_centos_artifact:
-    needs: [create_release]
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout repo
-        uses: actions/checkout@v4
-
-      - name: Build Docker image
-        run: docker build -t linux -f .github/workflows/Dockerfile.centos .
-
-      - name: Create container
-        run: docker create --name linuxcontainer linux
-
-      - name: Copy executable
-        run: docker cp linuxcontainer:/root/.local/bin/pileupCaller pileupCaller-conda-linux
-
-      - name: Upload Release Asset
-        id: upload-release-asset
-        uses: ncipollo/release-action@v1
-        with:
-          name: Release ${{ github.ref_name }}
-          draft: true
-          allowUpdates: true
-          artifactErrorsFailBuild: true
-          artifacts: pileupCaller-conda-linux
-          artifactContentType: application/octet-stream
+  # build_centos_artifact:
+  #   needs: [create_release]
+  #   runs-on: ubuntu-latest
+
+  #   steps:
+  #     - name: Checkout repo
+  #       uses: actions/checkout@v4
+
+  #     - name: Build Docker image
+  #       run: docker build -t linux -f .github/workflows/Dockerfile.centos .
+
+  #     - name: Create container
+  #       run: docker create --name linuxcontainer linux
+
+  #     - name: Copy executable
+  #       run: docker cp linuxcontainer:/root/.local/bin/pileupCaller pileupCaller-conda-linux
+
+  #     - name: Upload Release Asset
+  #       id: upload-release-asset
+  #       uses: ncipollo/release-action@v1
+  #       with:
+  #         name: Release ${{ github.ref_name }}
+  #         draft: true
+  #         allowUpdates: true
+  #         artifactErrorsFailBuild: true
+  #         artifacts: pileupCaller-conda-linux
+  #         artifactContentType: application/octet-stream

Changelog.md

@@ -1,5 +1,7 @@
 # Changelog
 
+- V 1.6.0.0: 
+    - pileupCaller now supports writing of VCF (Variant Call Format), via the standard output. See option --vcf and the Readme.
 - V 1.5.4.0:
    - updated sequence-formats dependency allows more lenient parsing of pileup-data, now also allowing for arbitrary reference alleles (not just ACTGN). This won't affect calling (reads that support an allele that is not in the SNP-file input are treated as before), but will be less disruptive when parsing pileup-input, for example without a bed-file in samtools.
    - improved error output for parsing problems with pileup-format data. Now only a small part of the problematic chunk is output, hopefully easing error interpretation in such cases