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marcelm / cutadapt

Cutadapt removes adapter sequences from sequencing reads
https://cutadapt.readthedocs.io
MIT License
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Crash on sending interleaved output to stdout #773

Closed marcelm closed 3 months ago

marcelm commented 3 months ago

Originally posted by @Jerrythafast in https://github.com/marcelm/cutadapt/issues/772#issuecomment-2018424356

$ cutadapt --interleaved tests/data/paired.1.fastq tests/data/paired.2.fastq
This is cutadapt 4.8.dev2+g9093ef7.d20240325 with Python 3.12.2
Command line parameters: --interleaved tests/data/paired.1.fastq tests/data/paired.2.fastq
Traceback (most recent call last):
  File ".../bin/cutadapt", line 8, in <module>
    sys.exit(main_cli())
             ^^^^^^^^^^
  File ".../cutadapt/src/cutadapt/cli.py", line 1132, in main_cli
    main(sys.argv[1:])
  File ".../cutadapt/src/cutadapt/cli.py", line 1212, in main
    pipeline = make_pipeline_from_args(
               ^^^^^^^^^^^^^^^^^^^^^^^^
  File ".../cutadapt/src/cutadapt/cli.py", line 902, in make_pipeline_from_args
    outfiles.open_record_writer(*paths, interleaved=interleaved)
  File ".../cutadapt/src/cutadapt/files.py", line 260, in open_record_writer
    assert path is not None
AssertionError

With -o out.fastq added to the command, there is no crash.