Review: Indexlr phred filter

bcgsc / btllib

Bioinformatics Technology Lab common code library

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Review: Indexlr phred filter #59

Closed aafshinfard closed 1 year ago

aafshinfard commented 2 years ago

We may avoid merging until we test various statistics and approaches to filter the kmers.

It now compiles alright using meson build & cd build & ninja
Running ninja quality-assurance throughs too many errors, as it does for the master branch
Running each ninja command independently it passes all except for ninja test-wrappers and ninja clang-tidy; The former throughs the following error and the latter throughs like 2500 lines of errors like ninja quality-assurance

aafshinfard commented 2 years ago


$ ninja test-wrappers
[0/1] Running external command test-wrappers (wrapped by meson to set env)
/projects/btl_scratch/aafshinfard/projects/indexlr/btllib/scripts/test-wrappers: line 12: cd: install/lib/btllib/python: No such file or directory
while executing ['/projects/btl_scratch/aafshinfard/projects/indexlr/btllib/scripts/test-wrappers']
FAILED: meson-internal__test-wrappers
/projects/btl/aafshinfard/miniconda3/envs/btllibpy37/bin/meson --internal exe --unpickle /projects/btl_scratch/aafshinfard/projects/indexlr/btllib/build/meson-private/meson_exe_test-wrappers_13ab3b46c63c92ffe82a617a047ad74450511228.dat
ninja: build stopped: subcommand failed.

aafshinfard commented 2 years ago

Having some weird issues locally with ninja quality-assurance just like a few other people in the lab. Trying to troubleshoot using the online Azure log.

aafshinfard commented 2 years ago

Tests passing now. I tried to make sure that wherever I update a constructor for q (quality), I keep another copy of that constructor without q so that older codes using newer btllib would not break.