v 1.2.3 release

.github/workflows/release.yml

@@ -0,0 +1,87 @@
+name: Create Release from setup.py
+
+on:
+  pull_request:
+    types:
+      - closed
+    branches:
+      - master
+
+jobs:
+  release:
+    if: github.event.pull_request.merged == true
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y poppler-utils
+
+
+      - name: Upgrade pip, setuptools, packaging and install git-cliff
+        run: |
+          python -m pip install --upgrade pip setuptools packaging 
+          pip install git-cliff
+
+      - name: Extract version from setup.py
+        id: get_version
+        run: |
+          VERSION=$(python setup.py --version)
+          echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Get latest release tag
+        id: get_last_release
+        run: |
+          latest=$(curl -s \
+            -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+            https://api.github.com/repos/${{ github.repository }}/releases/latest \
+            | jq -r '.tag_name' | sed 's/^v//')
+          echo "LATEST_RELEASE=$latest" >> $GITHUB_ENV
+
+      - name: Check release version
+        run: |
+          echo "New version: ${{ steps.get_version.outputs.VERSION }}"
+          echo "Latest release: $LATEST_RELEASE"
+          python - <<EOF
+          from packaging.version import parse
+
+          new_version = parse("${{ steps.get_version.outputs.VERSION }}")
+          latest_version = parse("$LATEST_RELEASE")
+
+          if new_version <= latest_version:
+              raise SystemExit(f"Error: New version ({new_version}) is not higher than latest release ({latest_version})")
+          EOF
+
+      - name: Generate CHANGELOG.md with git-cliff
+        run: |
+          git-cliff --unreleased --strip all --tag "v${{ steps.get_version.outputs.VERSION }}" > CHANGELOG.md
+
+      - name: Create Git tag
+        run: |
+          git config user.name "github-actions"
+          git config user.email "[email protected]"
+          git tag v${{ steps.get_version.outputs.VERSION }}
+          git push origin v${{ steps.get_version.outputs.VERSION }}
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          tag_name: v${{ steps.get_version.outputs.VERSION }}
+          body_path: CHANGELOG.md
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+
+

MANIFEST.in

@@ -0,0 +1 @@
+include SigProfilerClusters/controllers/*

SigProfilerClusters/SigProfilerClusters.py

@@ -639,6 +639,8 @@ def analysis(
     max_cpu=None,
     subClassify=False,
     variant_caller="standard",
+    tumor_vaf_column = 10, 
+    vaf_field = "AF",
     includedVAFs=True,
     includedCCFs=False,
     windowSize=1000000,
@@ -674,7 +676,9 @@ def analysis(
                                 -> caveman: If your VAF is recorded in the 11th column of your VCF as the last number of the colon delimited values, set variant_caller="caveman".
                                 -> standard: If your VAF is recorded in the 8th or 10th column of your VCF as VAF=xx or AF=xx, set variant_caller="standard".
                                 -> mutect2: If your VAF is recorded in the 10th or 11th column of your VCF as AF=xx, set variant_caller="mutect2".
-
+                                -> custom: Configure tumor_vaf_column as 0 based index (Default = 10) and the vaf_field tag (Default = AF)
+            tumor_vaf_column -> Activated when variant_caller = "custom". 0 based index of the column in VCF containing VAF (Default 10)
+            vaf_field       -> Activated when variant_caller = "custom". Set the VAF tag (Default AF)
 
                includedVAFs ->  optional parameter that informs the tool of the inclusion of VAFs in the dataset (boolean; default=True)
                includedCCFs ->  optional parameter that informs the tool of the inclusion of cancer cell fractions in the dataset (boolean; default=True)
@@ -1348,7 +1352,7 @@ def analysis(
             print("Beginning subclassification of clustered mutations...", end="")
             if includedVAFs:
                 classifyFunctions.pullVaf(
-                    project, input_path, variant_caller, correction
+                    project, input_path, variant_caller, tumor_vaf_column, vaf_field, correction
                 )
                 sys.stderr.close()
                 sys.stderr = open(error_file, "a")

SigProfilerClusters/SigProfilerHotSpots.py

@@ -478,6 +478,8 @@ def analysis(
     max_cpu=None,
     subClassify=False,
     variant_caller="standard",
+    tumor_vaf_column=10, 
+    vaf_field = "AF",
     includedVAFs=True,
     windowSize=1000000,
     bedRanges=None,
@@ -511,6 +513,9 @@ def analysis(
                                 -> caveman: If your VAF is recorded in the 11th column of your VCF as the last number of the colon delimited values, set variant_caller="caveman".
                                 -> standard: If your VAF is recorded in the 8th or 10th column of your VCF as VAF=xx or AF=xx, set variant_caller="standard".
                                 -> mutect2: If your VAF is recorded in the 10th or 11th column of your VCF as AF=xx, set variant_caller="mutect2".
+                                -> custom: Configure tumor_vaf_column as 0 based index (Default = 10) and the vaf_field tag (Default = AF)
+            tumor_vaf_column -> Activated when variant_caller = "custom". 0 based index of the column in VCF containing VAF (Default 10)
+            vaf_field       -> Activated when variant_caller = "custom". Set the VAF tag (Default AF)
                includedVAFs ->  optional parameter that informs the tool of the inclusion of VAFs in the dataset (boolean; default=True)
                      windowSize	->	the size of the window used for correcting the IMDs based upon mutational density within a given genomic range (integer; default=10000000)
               plotIMDfigure	->	optional parameter that generates IMD and mutational spectra plots for each sample (boolean; default=True).
@@ -1166,7 +1171,7 @@ def analysis(
             print("Beginning subclassification of clustered mutations...", end="")
             if includedVAFs:
                 classifyFunctions.pullVaf(
-                    project, input_path, variant_caller, correction
+                    project, input_path, variant_caller, tumor_vaf_column, vaf_field, correction
                 )
                 sys.stderr.close()
                 sys.stderr = open(error_file, "a")