fix: return error when bgzf_open fails to open a file #444
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* Before `rust_htslib::bgzf:Reader` and `rust_htslib::bgzf:Writer`
would never fail when opening a file that could not be opened
and it would allow writing to `rust_htslib::bgzf:Writer` without
returning any error messages.
johanneskoester
approved these changes
Nov 12, 2024
Pull Request Test Coverage Report for Build 11799735471Details
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ghuls
added a commit
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Nov 12, 2024
…files. Trow error if `scatac_from_fragments split` can't write to fragments files, by updating rust_htslib as both `rust_htslib::bgzf:Reader` and `rust_htslib::bgzf:Writer` did not check if it could open a file successfully. rust-bio/rust-htslib#444 This now print a traceback instead of silently failing: Processing contig "chr1" thread '<unnamed>' panicked at src/split_fragments.rs:56:37: Could not open file "/tmp/sample1/cellA.fragments.tsv.gz" for writing note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace Traceback (most recent call last): File "/software/anaconda3/envs/pycistopic/bin/scatac_fragment_tools", line 8, in <module> sys.exit(main()) ^^^^^^ File "/software/scatac_fragment_tools/src/scatac_fragment_tools/cli/main.py", line 317, in main args.func(args) File "/software/scatac_fragment_tools/src/scatac_fragment_tools/cli/commands.py", line 186, in command_split_fragments_by_cell_type split_fragment_files_by_cell_type( File "/software/scatac_fragment_tools/src/scatac_fragment_tools/library/split/split_fragments_by_cell_type.py", line 79, in split_fragment_files_by_cell_type joblib.Parallel(n_jobs=n_cpu)( File "/software/anaconda3/envs/pycistopic/lib/python3.11/site-packages/joblib/parallel.py", line 1918, in __call__ return output if self.return_generator else list(output) ^^^^^^^^^^^^ File "/software/anaconda3/envs/pycistopic/lib/python3.11/site-packages/joblib/parallel.py", line 1847, in _get_sequential_output res = func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ pyo3_runtime.PanicException: Could not open file "/tmp/sample1/cellA.fragments.tsv.gz" for writing
ghuls
added a commit
to aertslab/scatac_fragment_tools
that referenced
this pull request
Nov 12, 2024
… files. Throw error if `scatac_from_fragments split` can't write to fragments files, by updating rust_htslib as both `rust_htslib::bgzf:Reader` and `rust_htslib::bgzf:Writer` did not check if it could open a file successfully. rust-bio/rust-htslib#444 This now print a traceback instead of silently failing: Processing contig "chr1" thread '<unnamed>' panicked at src/split_fragments.rs:56:37: Could not open file "/tmp/sample1/cellA.fragments.tsv.gz" for writing note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace Traceback (most recent call last): File "/software/anaconda3/envs/pycistopic/bin/scatac_fragment_tools", line 8, in <module> sys.exit(main()) ^^^^^^ File "/software/scatac_fragment_tools/src/scatac_fragment_tools/cli/main.py", line 317, in main args.func(args) File "/software/scatac_fragment_tools/src/scatac_fragment_tools/cli/commands.py", line 186, in command_split_fragments_by_cell_type split_fragment_files_by_cell_type( File "/software/scatac_fragment_tools/src/scatac_fragment_tools/library/split/split_fragments_by_cell_type.py", line 79, in split_fragment_files_by_cell_type joblib.Parallel(n_jobs=n_cpu)( File "/software/anaconda3/envs/pycistopic/lib/python3.11/site-packages/joblib/parallel.py", line 1918, in __call__ return output if self.return_generator else list(output) ^^^^^^^^^^^^ File "/software/anaconda3/envs/pycistopic/lib/python3.11/site-packages/joblib/parallel.py", line 1847, in _get_sequential_output res = func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ pyo3_runtime.PanicException: Could not open file "/tmp/sample1/cellA.fragments.tsv.gz" for writing
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rust_htslib::bgzf:Readerandrust_htslib::bgzf:Writerwould never fail when opening a file that could not be opened and it would allow writing torust_htslib::bgzf:Writerwithout returning any error messages.