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Update lib/galaxy/datatypes/binary.py
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
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lib/galaxy/datatypes/binary.py

Lines changed: 1 addition & 1 deletion
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@@ -933,7 +933,7 @@ def set_meta(
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extra_threads = int(os.environ.get("GALAXY_SLOTS", 1)) - 1
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if index_flag == "-b":
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# IOError: No such file or directory: '-b' if index_flag is set to -b (pysam 0.15.4)
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pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name()) # type: ignore[attr-defined, unused-ignore]
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pysam.index("-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())
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else:
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pysam.index(index_flag, "-o", index_file.get_file_name(), f"-@{extra_threads}", dataset.get_file_name())
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dataset.metadata.bam_index = index_file

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