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tenx/metrics: fix 'reads_in_cells' for Cellranger 10 immune profiling output.
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Lines changed: 6 additions & 5 deletions

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auto_process_ngs/tenx/metrics.py

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -425,11 +425,12 @@ def reads_in_cells(self):
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"""
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Returns the number of reads in cells
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"""
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try:
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# Cellranger 10
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return self.fetch('Number of reads in cells')
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except MissingMetricError:
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pass
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# Cellranger 10
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for library_type in ("Gene Expression", "Antibody Capture"):
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try:
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return self.fetch('Number of reads in cells', library_type)
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except (KeyError, MissingMetricError):
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pass
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try:
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# Cellranger <= 9
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return self.fetch('Number of reads from cells called from this sample')

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