Merge branch 'develop' into 'main'

release 1.0.0

See merge request casm/team78/hairpin-core!11

Author: blex-max

.gitignore

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+data*
+.env/
+venv/
+.venv/
+dist/
+*.egg-info/
+__pycache__/
+.helix/
+build/
+test_data_creation/
+*.txt
+*.sif
+*.json
+poetry.lock
+.coverage
+test/sim-data/
+test/old_*

.gitlab-ci.yml

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+stages:
+  - build
+  - test
+  - publish
+
+include:
+# DOCS: https://gitlab.internal.sanger.ac.uk/team113sanger/common/cicd-template/-/blob/develop/README.md
+  - project: 'team113sanger/common/cicd-template'
+    ref: 0.3.1
+    file: '.gitlab-ci-components.yml'
+
+#############
+# TEMPLATES #
+#############
+
+.generic-wo-script-or-rules:
+  extends:
+    - .component-variables
+    - .component-before_script
+    - .component-tags-shared-large-runner
+
+.specific-variables:
+  variables:
+    UNIT_TEST_MOUNT_POINT: /opt/tests
+    RUN_SCRIPT_MOUNT_POINT: /tmp/run.sh
+    # We need to set this to 1 to enable BuildKit as the Dockerfile uses BuildKit features to speed up the build
+    DOCKER_BUILDKIT: 1
+    PRE_FETCH_BASE_IMAGE: python:3.12-slim
+    # Incase 'docker compose' build is ever used we want to ensure the image
+    # does not have sudo. By default CICD jobs do not build with 'docker
+    # compose' but use 'docker' - so this is just a safety measure.
+    HAS_SUDO: 0
+
+############
+#   JOBS   #
+############
+
+build:
+  stage: build
+  extends:
+    - .generic-wo-script-or-rules
+    - .specific-variables
+    - .component-script_docker-build
+    - .component-rules-except-release
+
+unit-test:
+  stage: test
+  extends:
+    - .generic-wo-script-or-rules
+    - .specific-variables
+    - .component-rules-except-release
+  script:
+    - echo "*** [SCRIPT] START ***"
+    - echo "I am a script - I run the Python unit tests in a docker container"
+    - echo "Unit test against CANDIDATE_IMAGE='${CANDIDATE_IMAGE:?not-set-in-before_script}'"
+    - docker pull "${CANDIDATE_IMAGE}"
+    # Test image against unit tests - it requires env vars
+    - docker run --entrypoint "bash" -e TEST_DIR="${UNIT_TEST_MOUNT_POINT}" -v "${PWD}/test:${UNIT_TEST_MOUNT_POINT}:ro" -v "${PWD}/docker-run-unit-tests.sh:${RUN_SCRIPT_MOUNT_POINT}:ro" --rm "${CANDIDATE_IMAGE}" ${RUN_SCRIPT_MOUNT_POINT}
+    - echo "*** [SCRIPT] END ***"
+
+publish-develop:
+  stage: publish
+  extends:
+    - .generic-wo-script-or-rules
+    - .specific-variables
+    - .component-script-publish-develop-docker-image
+    - .component-rules-develop-only
+
+publish-tagged_and_latest_docker_images:
+  stage: publish
+  extends:
+    - .generic-wo-script-or-rules
+    - .specific-variables
+    - .component-script-publish-tagged+latest-docker-image
+    - .component-rules-tag-only
+

CHANGES.md

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+

Dockerfile

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+FROM python:3.12-slim
+
+# Set the working directory inside the container
+WORKDIR /hairpin2
+
+# Copy the current working directory contents into the container
+COPY . /hairpin2
+
+RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
+
+USER ubuntu
+WORKDIR /home/ubuntu
+
+# Install the hairpin package
+RUN pip install --no-warn-script-location /hairpin2
+
+ENV PATH=$PATH:/home/ubuntu/.local/bin
+
+# Define a test script to check the installation of hairpin
+RUN LOC=$(which hairpin2) \
+    && if [ -z "$LOC" ]; then \
+    echo "hairpin install failed" && exit 1; \
+    else echo "hairpin install successful"; fi
+
+# Set up the default command for the container
+ENTRYPOINT ["hairpin2"]
+

LICENSE

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+MIT License
+
+Copyright (C) 2024 Genome Research Ltd.
+
+Author: Alex Byrne <ab63@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+Bootstrap: docker
+From: python:3.12-slim
+
+%files
+. hairpin2/
+
+%post
+pip install --root-user-action ignore hairpin2/
+
+%test
+	LOC=$(which hairpin2)
+	if [ -z "$LOC"]; then
+		echo "hairpin install failed"
+	else
+		echo "hairpin install successful"
+	fi
+
+%runscript
+	exec hairpin2 "$@"

Singularity.def

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+#!/bin/bash
+
+if [ -z ${TEST_DIR} ]; then
+    echo "TEST_DIR not set!"
+    exit 1
+fi
+PKG_DIR=$(python -c "import os;import hairpin2;import inspect;print(os.path.dirname(inspect.getfile(hairpin2)))")
+
+echo "$(python --version)"
+echo "Package source directory: ${PKG_DIR}"
+
+pip install \
+    pytest==8.2.2 \
+    pytest-cov==5.0.0 \
+    pysam==0.22 && \
+pytest -m "validate" --cov="${PKG_DIR}" "${TEST_DIR}"
+

docker-run-unit-tests.sh

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+def _set_version() -> str:  # noqa: C901
+    """Set the package version from the project metadata in pyproject.toml."""
+    from warnings import warn
+
+    fallback_version = "0.0.0"
+    try:
+        # importlib.metadata is present in Python 3.8 and later
+        import importlib.metadata as importlib_metadata
+    except ImportError:
+        # use the shim package importlib-metadata pre-3.8
+        import importlib_metadata as importlib_metadata
+
+    try:
+        # __package__ allows for the case where __name__ is "__main__"
+        version = importlib_metadata.version(__package__ or __name__)
+    except importlib_metadata.PackageNotFoundError:
+        version = fallback_version
+
+    if version == fallback_version:
+        msg = (
+            f"Package version will be {fallback_version} because Python could not find "
+            f"package {__package__ or __name__} in project metadata. Either the "
+            "version was not set in pyproject.toml or the package was not installed. "
+            "If developing code, please install the package in editable "
+            "mode with `poetry install` or `pip install -e .`"
+        )
+        warn(msg)
+    return version
+
+
+__version__ = _set_version()

hairpin2/__init__.py

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+# hairpin2
+#
+# Copyright (C) 2024 Genome Research Ltd.
+#
+# Author: Alex Byrne <ab63@sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from enum import IntEnum, Flag
+from typing import Callable
+import dataclasses as d
+
+EXIT_SUCCESS = 0
+EXIT_FAILURE = 1
+
+DEFAULTS: dict[str, int | float] = dict((('al_filter_threshold', 0.93),
+                                         ('min_clip_quality', 35),
+                                         ('min_mapping_quality', 11),
+                                         ('min_base_quality', 25),
+                                         ('max_read_span', 6),
+                                         ('edge_definition', 0.15),
+                                         ('edge_fraction', 0.9),
+                                         ('min_MAD_one_strand', 0),
+                                         ('min_sd_one_strand', 4),
+                                         ('min_MAD_both_strand_weak', 2),
+                                         ('min_sd_both_strand_weak', 2),
+                                         ('min_MAD_both_strand_strong', 1),
+                                         ('min_sd_both_strand_strong', 10),
+                                         ('min_reads', 1)))
+
+FiltCodes = IntEnum('FiltCodes',
+                    ['SIXTYAI',
+                     'SIXTYBI',
+                     'ON_THRESHOLD',
+                     'INSUFFICIENT_READS',
+                     'NO_MUTANTS'],
+                    start=0)
+Ops = IntEnum('Ops',
+              ['MATCH',
+               'INS',
+               'DEL',
+               'SKIP',
+               'SOFT',
+               'HARD',
+               'PAD',
+               'EQUAL',
+               'DIFF',
+               'BACK'],
+              start=0)
+ValidatorFlags = Flag('ValidatorFlags',
+                      ['CLEAR',
+                       'FLAG',
+                       'MAPQUAL',
+                       'READ_FIELDS_MISSING',
+                       'NOT_ALIGNED',
+                       'BAD_OP',
+                       'NOT_ALT',
+                       'BASEQUAL',
+                       'SHORT',
+                       'CLIPQUAL',
+                       'OVERLAP'],
+                      start=0)
+
+
+class NoAlts(ValueError):
+    pass
+
+
+class NoMutants(ValueError):
+    pass
+
+
+@d.dataclass
+class FilterData:
+    name: str
+    flag: bool = False
+    code: int | None = None
+
+    def set(self):
+        self.flag = True
+
+    def __iter__(self):
+        return (getattr(self, field.name) for field in d.fields(self))
+
+
+@d.dataclass
+class ADFilter(FilterData):
+    name: str = d.field(default='ADF')
+
+
+@d.dataclass
+class ALFilter(FilterData):
+    name: str = d.field(default='ALF')
+    avg_as: float | None = None
+
+
+@d.dataclass
+class Filters:
+    AL: ALFilter
+    HP: ADFilter
+
+    def __iter__(self):
+        return (getattr(self, field.name) for field in d.fields(self))
+
+    def fill_field(self, field_name, value):
+        if hasattr(self, field_name):
+            setattr(self, field_name, value)
+        else:
+            raise AttributeError
+
+    def get_field(self, field_name):
+        if hasattr(self, field_name):
+            return getattr(self, field_name)
+        else:
+            raise AttributeError
+
+
+FiltReturn = Callable[..., Filters]
+FlagReturn = Callable[..., int]