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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 python library incorrectly reporting NovaSeq flowcell surfaces count #280

Closed ppswang closed 2 years ago

ppswang commented 2 years ago

Hi,

I have a set of NovaSeq 6000 flowcell data that was provided to me by Illumina.

This looks to be an SP flowcell:

RunParameters.xml:    <FlowCellMode>SP</FlowCellMode>
RunParameters.xml:    <ClusterSupportedModes>SP</ClusterSupportedModes>

The number of tiles reported in RunInfo.xml is 312, which matches the specifications for SP flowcell. According to the specs, the number of surfaces should be 1 for a SP flowcell.

However, when I tried to get this information with the following:

from interop import py_interop_run
run = py_interop_run.info()
run.read(FCDIR)
interop_fc = run.flowcell()

interop_fc.surface_list() returned (2,) while interop_fc.surface_count() returned 2

ezralanglois commented 2 years ago

This is due to a limitation in our legacy plotting library. We label each surface 1 and 2, if only surface 2 is scanned, then we still report the surface count as 2.

This logic could be moved downstream. Really, getting the length of the surface list is a better way to determine the number of surfaces.