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Addition of multithreading #419

Merged
merged 87 commits into from
Nov 15, 2024
Merged

Addition of multithreading #419

merged 87 commits into from
Nov 15, 2024

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nickjcroucher
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Fix CI problems and enable multithreading of recombination detection.

@nickjcroucher
Optimise recombination identification
fbb5df9
@nickjcroucher
Merge pull request #404 from nickjcroucher/master
ec400bd 
Update branch with optimised C code
@nickjcroucher
Fix comment typo
dc34d59
@nickjcroucher
Restore master version to check CI
2e0cfa5
@nickjcroucher
Restore filtering block functions
afd8aed
@nickjcroucher
Update get_blocks function
28fcdb2
@nickjcroucher
Update downstream recombinations function
899a885
@nickjcroucher
Revert "Update get_blocks function"
37a5d36 
This reverts commit 28fcdb2.
@nickjcroucher
Add tree iteration functions
e32c59f
@nickjcroucher
Access lists of nodes at different depths
c7c0f77
@nickjcroucher
Revert breaking changes
88056ef
@nickjcroucher
Prototype multithreading function
0c75025
@nickjcroucher
Remove node counter
98a8854
@nickjcroucher
Rename variables to help rewrite
8865558
@nickjcroucher
Introduce new data structures
da4470c
@nickjcroucher
Switch recursion to loop
11385bd
@nickjcroucher
Correct indentation of sequence storage
73307e4
@nickjcroucher
Add pthreads to compilation commands
8ceba52
@nickjcroucher
Correct length of sequence stored
0bf08b1
@nickjcroucher
Correct array parsing
fbd7e33
@nickjcroucher
Fix conditional test
02e5201
@nickjcroucher
Fix NULL initialisation
9d458a5
@nickjcroucher
Fix memory clearing error
16ae012
@nickjcroucher
Fix memory allocation statements
fdb338e
@nickjcroucher
Update ordering of file with new function implementation
7fa1eb1
@nickjcroucher
Changes to formatting
5d97efb
@nickjcroucher
Multithread branch sequence reconstruction
abb28ac
@nickjcroucher
Remove potential memory leaks
a41030f
@nickjcroucher
Update memory management
d90ba08
@nickjcroucher
Simplify code structure
28cf4fd
@nickjcroucher
Add stats test
eb630fa
@nickjcroucher
Parallelise gap function
15fabaa
@nickjcroucher
Set values by index not name
e298ad3
@nickjcroucher
Avoid copying nodes when parallelising
57d1863
@nickjcroucher
Update IQTREE multithreading argument
4b2488f
@nickjcroucher
Add ska.rust citation
d5091b5
@nickjcroucher
Change CI for new OSX version
facb8db
@nickjcroucher
Change CI again for new OSX version
da5cf49
@nickjcroucher
Remove chown command
bbb2c8c
@nickjcroucher
Add miniconda installation
0f2f560
@nickjcroucher
Change miniconda installation
8b867ff
@nickjcroucher
Change CI file indentation
f4dac82
@nickjcroucher
Downgrade macos until dependencies upgraded
29d1792
@nickjcroucher
Change line width based on number of samples
cf77eaa
@nickjcroucher
Add script for extracting recombinant sequences
d13ff7f
@nickjcroucher
Add extract_recombinant_sequences.py
f6843ef
@nickjcroucher
Make script executable
86f189a
@nickjcroucher
Add test_extract_recombination_sequences
7a1218a
@nickjcroucher
Add documentation for extract_recombinant_sequences.py
04f27d8
@nickjcroucher
Improve AVX RAxML selection
13f1e64
@nickjcroucher
Fix calculation of recombination lengths
5777717
@nickjcroucher
Enable recombination length calculation with gaps
d2ed906
@nickjcroucher
Calculate recombination length including gaps
b2135ab
@nickjcroucher
Add argument to calculate_number_of_bases_in_recombinations_excluding…
df8e440 
…_gaps
@nickjcroucher
Update function name
4ecbd72
@nickjcroucher
Test if rec length tests cause failure
4bd91a5
@nickjcroucher
Test if rec length tests cause failure
b0ddb28
@nickjcroucher
Update expected stats file
98aa8fc
@nickjcroucher
Restore rec length tests
8ca358f
@nickjcroucher nickjcroucher merged commit 7645c64 into master Nov 15, 2024
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@nickjcroucher