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Fix error where missing qualities in BAM file were not properly converted #535

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Fix error where missing qualities in BAM file were not properly converted

Fix error where missing qualities in BAM file were not properly converted #535

Triggered via pull request October 4, 2024 07:31
@rhpvordermanrhpvorderman
synchronize #195
missingquals
Status Success
Total duration 2m 34s
Artifacts –

ci.yml

on: pull_request
Matrix: package-checks
Matrix: test
test-arch
0s
test-arch
Matrix: deploy
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1 error and 48 warnings
test (macos-latest, 3.8)
[notice] A new release of pip is available: 21.1.1 -> 24.2 [notice] To update, run: python3.8 -m pip install --upgrade pip
package-checks (pedantic_compile)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
package-checks (pedantic_compile)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
package-checks (pedantic_compile)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
package-checks (twine_check)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
package-checks (twine_check)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
package-checks (twine_check)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
package-checks (docs)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
package-checks (docs)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
package-checks (docs)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
package-checks (lint)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
package-checks (lint)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
package-checks (lint)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
package-checks (html5validator)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
package-checks (html5validator)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
package-checks (html5validator)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (macos-latest, 3.12)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (macos-latest, 3.12)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (macos-latest, 3.12)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (macos-latest, 3.8)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (macos-latest, 3.8)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (macos-latest, 3.8)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (3.9, ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (3.9, ubuntu-latest)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (3.9, ubuntu-latest)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (3.11, ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (3.11, ubuntu-latest)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (3.11, ubuntu-latest)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (3.8, ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (3.8, ubuntu-latest)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (3.8, ubuntu-latest)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (3.10, ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (3.10, ubuntu-latest)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (3.10, ubuntu-latest)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (3.12, ubuntu-latest)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (3.12, ubuntu-latest)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (3.12, ubuntu-latest)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (macos-13, 3.8)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (macos-13, 3.8)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (macos-13, 3.8)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (macos-13, 3.12)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (macos-13, 3.12)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (macos-13, 3.12)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (windows-latest, 3.8)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (windows-latest, 3.8)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (windows-latest, 3.8)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
test (windows-latest, 3.12)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
test (windows-latest, 3.12)
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/setup-python@v2.2.1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
test (windows-latest, 3.12)
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/