44 lines
1.2 KiB
Python
Executable File
44 lines
1.2 KiB
Python
Executable File
"""Validate a single (u)BAM file index."""
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from pathlib import Path
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import sys
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import pysam
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from .util import get_named_logger, wf_parser # noqa: ABS101
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def validate_xam_index(xam_file):
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"""Use fetch to validate the index.
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Invalid indexes will fail the call with a ValueError:
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ValueError: fetch called on bamfile without index
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"""
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with pysam.AlignmentFile(xam_file, check_sq=False) as alignments:
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try:
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alignments.fetch()
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has_valid_index = True
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except ValueError:
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has_valid_index = False
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return has_valid_index
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def main(args):
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"""Run the entry point."""
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logger = get_named_logger("checkBamIdx")
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# Check if a XAM has a valid index
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has_valid_index = validate_xam_index(args.input_xam)
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# write `has_valid_index` out so that they can be set as env.
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sys.stdout.write(
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f"HAS_VALID_INDEX={int(has_valid_index)}"
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)
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logger.info(f"Checked (u)BAM index for: '{args.input_xam}'.")
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def argparser():
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"""Argument parser for entrypoint."""
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parser = wf_parser("check_xam_index")
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parser.add_argument("input_xam", type=Path, help="Path to target XAM")
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return parser
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