1.0.3

.github/workflows/release.yml

@@ -0,0 +1,118 @@
+name: Build and Release
+
+on:
+  push:
+    tags:
+      - 'v*'  # Triggers the workflow when a tag starting with 'v' is pushed
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]  # build for ubuntu and mac
+        arch: [x64, arm64] # x64 and arm
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up build environment
+        run: |
+          if [ ${{ matrix.os }} == 'ubuntu-latest' ]; then
+            sudo apt-get update
+            sudo apt-get install -y autoconf gcc make
+          elif [ ${{ matrix.os }} == 'macos-latest' ]; then
+            brew install autoconf gcc make
+          fi
+
+      - name: Build
+        run: |
+          make
+          mkdir -p installation/usr/local/bin
+          cd src && make install DESTDIR=../installation
+
+      - name: Extract version from github.ref
+        id: extract_version
+        run: echo "::set-output name=version::$(echo ${GITHUB_REF#refs/tags/})"
+
+      - name: Create tar.gz archive
+        run: |
+          cd installation/usr/local/bin
+          tar -czvf ../../../HELLO-${{ steps.extract_version.outputs.version }}.${{ matrix.os }}.${{ matrix.arch }}.tar.gz hello
+
+      - name: Archive build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: HELLO-${{ matrix.os }}-${{ matrix.arch }}
+          path: installation/HELLO-${{ steps.extract_version.outputs.version }}.${{ matrix.os }}.${{ matrix.arch }}.tar.gz
+          if-no-files-found: error
+
+  release:
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        arch: [x64, arm64]
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Check if release exists
+        id: check_release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref_name }}
+        run: |
+          if gh release view "$tag" --repo="$GITHUB_REPOSITORY" > /dev/null 2>&1; then
+            echo "release_exists=true" >> $GITHUB_ENV
+          else
+            echo "release_exists=false" >> $GITHUB_ENV
+          fi
+
+      - name: Create release
+        if: env.release_exists == 'false'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref_name }}
+        run: |
+          gh release create "$tag" \
+              --repo="$GITHUB_REPOSITORY" \
+              --title="${GITHUB_REPOSITORY#*/} ${tag#v}" \
+              --generate-notes
+
+      - name: Download build artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: HELLO-${{ matrix.os }}-${{ matrix.arch }}
+          path: ./artifacts
+
+      - name: List files in artifacts directory
+        run: |
+          echo "Listing files in ./artifacts:"
+          ls -l ./artifacts
+
+      - name: Upload Release Assets
+        uses: softprops/action-gh-release@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          files: ./artifacts/HELLO-${{ matrix.os }}-${{ matrix.arch }}/*
+          tag_name: ${{ steps.extract_version.outputs.version }}
+          name: Release ${{ steps.extract_version.outputs.version }}
+          prerelease: false
+          draft: false
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'  # Specify the version of Python to use
+
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip && pip install requests
+
+      - name: Run Python script
+        run: |
+          python .github/workflows/update_release_table.py ${{ github.ref_name }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/update_release_table.py

@@ -0,0 +1,131 @@
+import requests
+import argparse
+import os
+import re
+
+# GitHub repository details
+# adjust REPO to match your setup
+REPO = "TravisWheelerLab/ULTRA"
+API_URL = f"https://api.github.com/repos/{REPO}/releases"
+
+def get_releases_data():
+    headers = {
+        'Authorization': f'token {os.getenv("GITHUB_TOKEN")}',
+        'Accept': 'application/vnd.github.v3+json',
+    }
+    response = requests.get(API_URL, headers=headers)
+    response.raise_for_status()
+    return response.json()
+
+def find_release_by_version(releases, version):
+    for release in releases:
+        if release["tag_name"] == version:
+            return release
+    return None
+
+def extract_os_arch_from_filename(filename):
+    pattern = r'[.-]([a-zA-Z]+-[a-zA-Z]+)\.([a-zA-Z0-9_]+)\.tar\.gz'
+
+    match = re.search(pattern, filename)
+
+    if match:
+        os = match.group(1)
+        arch = match.group(2)
+
+        if os == "macos-latest":
+            os = "MacOS"
+        elif os == "ubuntu-latest":
+            os = "Ubuntu"
+        elif os == "windows-latest":
+            os = "Windows"
+
+        if arch == "x64":
+            arch = "Intel/AMD 64-bit"
+        elif arch == "386":
+            arch = "Intel/AMD 32-bit"
+        elif arch == "arm64":
+            if os == "MacOS":
+                arch = "M1/M2/M3 (ARM 64-bit)"
+            else:
+                arch = "ARM 64-bit"
+        elif arch == "arm":
+            arch = "ARM 32-bit"
+
+        return os, arch
+    else:
+        return None, None
+
+def generate_markdown_table(release):
+    table = "### Release Assets\n"
+    table += "| OS | Architecture | Link |\n"
+    table += "|---------|----------|-------------|\n"
+
+    for asset in release["assets"]:
+        if not asset["name"].endswith(".md5"):
+            # parse
+            os, arch = extract_os_arch_from_filename(asset["name"])
+            download_url = asset["browser_download_url"]
+            table += f"| {os}  | {arch}  | [Download]({download_url}) |\n"
+
+    # Add note about Mac binary signing restriction
+    table += (
+        "\nTo address the Mac binary signing restriction, use the following command: "
+        "`sudo xattr -dr com.apple.quarantine <path to file>/my-binary-amd64`\n"
+    )
+
+    return table
+
+def update_release_body(release_id, new_body):
+    headers = {
+        'Authorization': f'token {os.getenv("GITHUB_TOKEN")}',
+        'Accept': 'application/vnd.github.v3+json',
+    }
+    update_url = f"https://api.github.com/repos/{REPO}/releases/{release_id}"
+    data = {
+        "body": new_body
+    }
+
+    response = requests.patch(update_url, headers=headers, json=data)
+    response.raise_for_status()
+
+"""
+def update_readme(table):
+    with open("README.md", "r") as file:
+        lines = file.readlines()
+
+    with open("README.md", "w") as file:
+        inside_table = False
+        for line in lines:
+            if line.startswith("| Version"):
+                inside_table = True
+                file.write(table)
+                continue
+            if inside_table and line.startswith("|"):
+                continue
+            file.write(line)
+"""
+
+def main(target_version):
+    releases = get_releases_data()
+    release_to_update = find_release_by_version(releases, target_version)
+
+    if release_to_update:
+        release_id = release_to_update["id"]
+        current_body = release_to_update.get("body", "")
+
+        markdown_table = generate_markdown_table(release_to_update)
+        print(markdown_table)
+
+        if "### Release Assets\n" not in current_body:
+            updated_body = current_body + "\n\n" + markdown_table
+            update_release_body(release_id, updated_body)
+            print(f"Release {target_version} updated successfully.")
+    else:
+        print(f"Release with version {target_version} not found.")
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Update a specific release in GitHub.")
+    parser.add_argument("version", help="The tag name of the release to update")
+    args = parser.parse_args()
+
+    main(args.version)

README.md

@@ -2,7 +2,7 @@
 
 **U**LTRA **L**ocates **T**andemly **R**epetitive **A**reas
 ## About
-ULTRA is a tool for finding and annotating tandem repeats within genomic sequence. Model details and evaluation can be found in our release paper, [ULTRA-Effective Labeling of Tandem Repeats in Genomic Sequence](https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1)
+ULTRA is a tool for finding and annotating tandem repeats within genomic sequence. Model details and evaluation can be found in our release paper, [ULTRA-Effective Labeling of Tandem Repeats in Genomic Sequence](https://academic.oup.com/bioinformaticsadvances/article/4/1/vbae149/7816237)
 
 ## Building
 ULTRA requires a compiler supporting C++11 or higher and CMake 3.12 or higher.  To download and build ULTRA run the following commands:
@@ -162,15 +162,18 @@ Here `examples/tune_file` tests different repeat periods (`-p <repeat period>`),
 
 ## Citing
 ```
-@article {Olson2024ultra,
-  author = {Olson, Daniel R. and Wheeler, Travis J.},
-  title = {ULTRA-Effective Labeling of Repetitive Genomic Sequence},
-  elocation-id = {2024.06.03.597269},
-  year = {2024},
-  doi = {10.1101/2024.06.03.597269},
-  publisher = {Cold Spring Harbor Laboratory},
-  URL = {https://www.biorxiv.org/content/early/2024/06/04/2024.06.03.597269},
-  eprint = {https://www.biorxiv.org/content/early/2024/06/04/2024.06.03.597269.full.pdf},
-  journal = {bioRxiv}
+@article{10.1093/bioadv/vbae149,
+    author = {Olson, Daniel R and Wheeler, Travis J},
+    title = {ULTRA-effective labeling of tandem repeats in genomic sequence},
+    journal = {Bioinformatics Advances},
+    volume = {4},
+    number = {1},
+    pages = {vbae149},
+    year = {2024},
+    month = {10},
+    issn = {2635-0041},
+    doi = {10.1093/bioadv/vbae149},
+    url = {https://doi.org/10.1093/bioadv/vbae149},
+    eprint = {https://academic.oup.com/bioinformaticsadvances/article-pdf/4/1/vbae149/60779841/vbae149.pdf},
 }
 ```

src/JSONFileWriter.cpp

@@ -91,9 +91,16 @@ void JSONFileWriter::WriteRepeat(RepeatRegion *repeat) {
     this->OutputJSONKeyValue("PVal", std::to_string(pval));
   }
 
-  this->OutputJSONKeyValue("Substitutions", std::to_string(repeat->mismatches));
-  this->OutputJSONKeyValue("Insertions", std::to_string(repeat->insertions));
-  this->OutputJSONKeyValue("Deletions", std::to_string(repeat->deletions));
+
+  if (owner->settings->show_counts) {
+    auto copies = (repeat->repeatLength - repeat->insertions + repeat->deletions) / repeat->repeatPeriod;
+    this->OutputJSONKeyValue("Copies", std::to_string(copies));
+    this->OutputJSONKeyValue("Substitutions",
+                             std::to_string(repeat->mismatches));
+    this->OutputJSONKeyValue("Insertions", std::to_string(repeat->insertions));
+    this->OutputJSONKeyValue("Deletions", std::to_string(repeat->deletions));
+  }
+
   this->OutputJSONKeyValue("Consensus", repeat->string_consensus, true);
 
   if (owner->settings->show_seq) {

src/TabFileWriter.cpp

@@ -20,6 +20,11 @@ void TabFileWriter::InitializeWriter(Ultra *ultra, FILE *out_f) {
     fprintf(out, ",PValue");
   if (owner->settings->max_consensus_period >= 0)
     fprintf(out, "\tConsensus");
+
+  if (owner->settings->show_counts) {
+    fprintf(out, "\t#copies\t#substitutions\t#insertions\t#deletions");
+  }
+
   if (owner->settings->max_split >= 0) {
     fprintf(out, "\t#Subrepeats");
     fprintf(out, "\tSubrepeatStarts");
@@ -31,6 +36,7 @@ void TabFileWriter::InitializeWriter(Ultra *ultra, FILE *out_f) {
     fprintf(out, "\tSequence");
   }
 
+
   fprintf(out, "\n");
 
 }
@@ -75,6 +81,12 @@ void TabFileWriter::WriteRepeat(RepeatRegion *repeat) {
     fprintf(out, "\t%s", rep_con.c_str());
   }
 
+  if (owner->settings->show_counts) {
+    auto copies = (repeat->repeatLength - repeat->insertions + repeat->deletions) / repeat->repeatPeriod;
+
+    fprintf(out, "\t%lu\t%d\t%d\t%d", copies, repeat->mismatches, repeat->insertions, repeat->deletions);
+  }
+
   if (owner->settings->max_split >= 0) {
     std::string sizes = "";
     std::string starts = "0";
@@ -138,6 +150,8 @@ void TabFileWriter::WriteRepeat(RepeatRegion *repeat) {
   if (owner->settings->show_seq) {
     fprintf(out, "\t%s", repeat->sequence.c_str());
   }
+
+
   fprintf(out, "\n");
 }