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Release 0.11.0#186

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rhpvorderman merged 41 commits intomainrhpvorderman/sequali:mainfrom release_0.10.1rhpvorderman/sequali:release_0.10.1Copy head branch name to clipboardAug 9, 2024

+60,665-9,164

Commits

Commits on Jun 3, 2024

• Update example report

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• Add datagathering benchmark option

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Commits on Jun 4, 2024

• Replace vector code with compiler auto optimizable code

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• Remove sse2 vectorization of base calls

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• Rewrite table with base definitions

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• Use different indices for nucleotides

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• Store basecounts in registers rather than memory

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• Write error accumulation in such a way that it can be auto vectorized

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Commits on Jun 5, 2024

• Add notice to changelog about the replaced vector code

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• Merge pull request #172 from rhpvorderman/autooptimalc

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Commits on Jun 7, 2024

• Add a report with cut adapters

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• Add a processed file to the documentation for before and after pics

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Commits on Jun 10, 2024

• Add illumina paired-end report

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• Add illumina paired-end report to the examples

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Commits on Jun 12, 2024

• Support prefetching on other architectures

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• Merge pull request #175 from rhpvorderman/prefetch

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Commits on Jun 30, 2024

• Simpler bam decoding

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• Simplify dynamic dispatch to load time dispatch

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• Do not finish vectorized loop prematurely

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• Merge pull request #177 from rhpvorderman/betternibble

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• Simplify GC counting slightly

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• Simplify by unifying AT and GC counter

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• Merge pull request #178 from rhpvorderman/bettergccount

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Commits on Jul 8, 2024

• Integrate clang-format in CI

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• Perform clang-format formatting

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• Add pre-commit hooks

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• Fix linting errors in scripts

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• Merge pull request #179 from rhpvorderman/clang-format

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• Proper include order

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• Simplified dispatch for sequence identity functions

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• Merge pull request #180 from rhpvorderman/betterdispatch

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Commits on Jul 9, 2024

• Add pre-commit to linting check to ensure uniformity

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• Use version from sequali directly

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• Merge pull request #181 from rhpvorderman/pre-commit-ci

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• Make plot ids reproducible

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Commits on Jul 10, 2024

• Merge pull request #183 from rhpvorderman/reproducibleuuid

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Commits on Aug 9, 2024

• Use floor rather than round for phred scores

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• Rewrite test so it is not dependent on platform dependent flooring

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• Merge pull request #184 from rhpvorderman/floornotround

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• Prepare release 0.10.1

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• Release number increased to 0.11.0 and documented all the important changes

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