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Illumina / interop

C++ Library to parse Illumina InterOp files
http://illumina.github.io/interop/index.html
GNU General Public License v3.0
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interop.py_interop_comm.incomplete_file_exception for runs with no indices/demultiplexing #341

Closed nicolazilio closed 3 months ago

nicolazilio commented 4 months ago

Hello there,

It appears that I can't open InterOp folders for runs where no demultiplexing occured, that is, where no indices were provided in the sample sheet

Traceback (most recent call last):
  File "/opt/pushParkourStats.py", line 112, in pushRunStats
    interop.read(
  File "/opt/conda/lib/python3.10/site-packages/interop/core.py", line 819, in read
    run_metrics = read_metric(filename, run_metrics=run_metrics, finalize=True)
  File "/opt/conda/lib/python3.10/site-packages/interop/core.py", line 849, in read_metric
    run_metrics.read_metrics_from_buffer(metric_group, data)
  File "/opt/conda/lib/python3.10/site-packages/interop/py_interop_run_metrics.py", line 334, in read_metrics_from_buffer
    return _py_interop_run_metrics.run_metrics_read_metrics_from_buffer(self, group, buffer)
interop.py_interop_comm.incomplete_file_exception: Insufficient data read from the file, got: 0 != expected: 9 for Index  v2
/io/./interop/io/format/metric_format.h::test_stream (250)

The offending line is this one.

I can provide you with an example, via DM.

ezralanglois commented 3 months ago

Incomplete file exception does not mean nothing was parsed. We normally catch and ignore this exception except when we expect the run to be complete.