Merge dev#14

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hannespetur wants to merge 44 commits intomasterfrom

Commits on Feb 2, 2021

global_alignment renamed to pairwise alignment
hannespetur
committed

Commits on Feb 17, 2021

Commits on Feb 18, 2021

allow O3 in avx512 (not sure why O1 was used). Improved performance of find_all_edits with very little tradeoffs
hannespetur
committed

Commits on Feb 26, 2021

skyr updates
hannespetur
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Commits on Mar 16, 2021

Added paw::station add_work_with_thread_id
hannespetur
committed

Commits on May 19, 2021

Commits on Sep 7, 2021

Also explicitly instantiate std::string_view when possible
hannespetur
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Commits on Sep 8, 2021

added ability to get cigar
hannespetur
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Commits on Sep 9, 2021

minor
hannespetur
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Commits on Sep 20, 2021

added all mismatches coding (X)
hannespetur
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Commits on Nov 3, 2021

support clipping when getting the cigar
hannespetur
committed

Commits on Nov 15, 2021

minor changes in clipping and cigar
hannespetur
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Commits on Nov 17, 2021

Added support for clipping_right only
hannespetur
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Commits on Jan 4, 2022

Added pairwise_ext_alignment
hannespetur
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Commits on Jan 7, 2022

Commits on Jan 10, 2022

Commits on Mar 25, 2022

added add_to_thread_with_thread_id
hannespetur
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Commits on Dec 1, 2022

Add CI for Linux ARM64

martin-g
authored and
hannespetur
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Make it possible to set custom arch related compilation options

martin-g
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hannespetur
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Add support for Arch::NEON to align.cpp

martin-g
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hannespetur
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Add a check for 'aarch64' ELF to the produced shared library in the CI

martin-g
authored and
hannespetur
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Run CI on 'push' event

martin-g
authored and
hannespetur
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Add option FORCE_NEON to the main CMakeLists.txt

martin-g
authored and
hannespetur
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Improve align example 2 to use neon on ARM64

martin-g
authored and
hannespetur
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Use a better CI job name

martin-g
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hannespetur
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Better check for archs in align2 example

martin-g
authored and
hannespetur
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Fix "Address boundary error" for ARM64_NEON

martin-g
authored and
hannespetur
committed

Commits on Aug 18, 2023

changed logic of N bases such that they are now considered to be mismatches
hannespetur
committed

Commits on Sep 26, 2023

added paw::Parser::get_raw_args_reference()
hannespetur
committed

Commits on Oct 10, 2023

Commits on Oct 18, 2023

modified skyr such that indels are represented together
hannespetur
committed

Commits on Oct 27, 2023

changed skyr logic, stopped using free SNPs since in some cases it was causing problems downstreams
hannespetur
committed

Commits on Oct 30, 2023

minor cleanup
hannespetur
committed