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As it turns out, when caIntegrator parses a mapping file where the same sample is mapped to multiple subjects and encounters a sample ID that has already been mapped, it will overwrite the old mapping with the new one. We can confirm this by clicking on the 'Map Samples' button for the source we mapped and examining the 'Samples Mapped to Subjects' table on the 'Edit Sample Mappings' page.
On the 'Edit Sample Mappings' page, sample ID 191 is only mapped to a single subject (highlighted in red), even though the mapping file we just loaded mapped that same sample twice.
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