Code

OS X build + integration tests#9

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Merged

iqbal-lab merged 77 commits intoiqbal-lab-org:masteriqbal-lab-org/cobs:masterfrom leoisl:macleoisl/cobs:macCopy head branch name to clipboardJul 14, 2022

+810-491

Commits

Commits on Jul 29, 2020

• Adding Dockerfile

  

  leandro

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Commits on Jul 30, 2020

• Adding cobs dir to PATH

  

  leandro

  committed
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Commits on Aug 5, 2020

• Improving container building with a simple script

  

  leandro

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Commits on Aug 25, 2021

• Adding ordering scripts

  leoisl

  committed
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Commits on Sep 8, 2021

• Transforming the numpy array as a 2-dimensional array to see if PIL can manage it

  leoisl

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• Adding time logging and removing compression methods that don't work

  leoisl

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Commits on Sep 10, 2021

• Several changes

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  leoisl

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• Adding some logging

  leoisl

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Commits on Sep 13, 2021

• Several changes

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  leoisl

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• Avoiding PIL.Image.DecompressionBombError error

  leoisl

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Commits on Sep 14, 2021

• Fixing bug in binary to images script and adding tests

  leoisl

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• Adding a script to check if the compressed index equals the original index

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  leoisl

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• No need to serialise the numpy object anymore

  leoisl

  committed
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Commits on Sep 16, 2021

• Small update to reorder_genomes

  leoisl

  committed
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Commits on Sep 21, 2021

• Now outputting transposed bf matrix

  leoisl

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Commits on Sep 27, 2021

• Adding first rules of xz_compressor snakemake pipeline

  leoisl

  committed
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• Merge remote-tracking branch 'leoisl/master' into ordering

  leoisl

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Commits on Sep 28, 2021

• Finishing snakemake pipeline

  leoisl

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Commits on Sep 29, 2021

• Fixing the submit_lsf script

  leoisl

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Commits on Nov 18, 2021

• Adding script to filter ordering to high quality genomes

  leoisl

  committed
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• Adding sample name to the random name in the pipeline

  leoisl

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Commits on Nov 23, 2021

• Support all fasta file extensions listed in Wikipedia

  jnalanko

  committed
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Commits on Nov 24, 2021

• Merge pull request bingmann#21 from jnalanko/master

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  bingmann

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• use python 3 for pybind11

  

  Timo Bingmann

  committed
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Commits on Jan 12, 2022

• Adding xor filter

  leoisl

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Commits on Mar 18, 2022

• size_t -> uint64_t

  leoisl

  committed
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• Fixing small issue

  leoisl

  committed
  9d0c0e0

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• Some other minor int types changes

  leoisl

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Commits on Mar 23, 2022

• Removing aio feature

  leoisl

  committed
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Commits on Mar 24, 2022

• Getting around _SC_PHYS_PAGES

  leoisl

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• Fixing some remaining typing issues

  leoisl

  committed
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• Fixing precompiler if else to get number of pages of physical memory

  leoisl

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• #elifdef not available on gcc11

  leoisl

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• Fixing some header issues

  leoisl

  committed
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• Type issue

  leoisl

  committed
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• Fixing phys_pages -> page_size

  leoisl

  committed
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• Making tests less strict (TODO: check if this is actually an ok solution)...

  leoisl

  committed
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Commits on Apr 4, 2022

• Merge remote-tracking branch 'leoisl/ordering' into mac

  leoisl

  committed
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• Changing last size_ts in code

  leoisl

  committed
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• unsigned long -> uint64_t

  leoisl

  committed
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• unsigned char -> uint8_t

  leoisl

  committed
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• int -> int64_t

  leoisl

  committed
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Commits on Apr 6, 2022

• fixing small compilation issue on getting nb of phys pages in mac

  leoisl

  committed
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Commits on Apr 11, 2022

• Fixing Mac issue by reading the COBS index in chunks of 1 GB

  leoisl

  committed
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Commits on Jun 15, 2022

• Revert "Making tests less strict (TODO: check if this is actually an ok solution)..."

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• Making tests less strict (TODO: check if this is actually an ok solution)...

  leoisl

  committed
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• Creating integration test script

  leoisl

  committed
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• Now using the 3 batches

  leoisl

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• Updating create_command_line.py

  leoisl

  committed
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Commits on Jun 16, 2022

• Updating integration tests command lines

  leoisl

  committed
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• Updating README

  leoisl

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• Adding README and results

  leoisl

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Commits on Jun 17, 2022

• Refactoring xz_compressor pipeline

  leoisl

  committed
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• Misc MD fixes

  leoisl

  committed
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• Misc MD fixes

  leoisl

  committed
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• Refactoring Snakefile

  leoisl

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• Linting

  leoisl

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• Cleaning up

  leoisl

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• Cleaning up

  leoisl

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• Cleaning up .gitignore

  leoisl

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• Adding aio back

  leoisl

  committed
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• Small reformatting

  leoisl

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• Small reformatting

  leoisl

  committed
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• Not compiling AIO if on Mac

  leoisl

  committed
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Commits on Jun 27, 2022

• Updating create_command_lines_run_on_cluster.py

  leoisl

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• Fixing create_command_lines_run_on_cluster.py

  leoisl

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• Fixing create_command_lines_run_on_cluster.py

  leoisl

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Commits on Jun 28, 2022

• Now comparing several query length results

  leoisl

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• Upgrading googletest

  leoisl

  committed
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• Refactoring some code from src/cobs.cpp to cobs/query/search.hpp

  leoisl

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• Adding mof integration tests

  leoisl

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Commits on Jul 1, 2022

• Merge remote-tracking branch 'iqbal-lab-org/master' into mac

  leoisl

  committed
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Commits on Jul 4, 2022

• Small refactoring

  leoisl

  committed
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• Making it compile with the new types

  leoisl

  committed
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• Fixing a bug introduced in classic_combine_streams() when merging

  leoisl

  committed
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• Cleanup, removing container building scripts

  leoisl

  committed
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Commits on Jul 5, 2022

• Updating integration batch test helpers

  leoisl

  committed
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