miscounting repeat number

[nbedelman]

Hello,
I am looking at a repeat locus that has two repetitive elements neighboring one another. My test pattern is "(TG)+(T)+", as there is a variable run of TG followed by a variable run of T. ExpansionHunter runs quickly, but generates output which differs from what can be seen through the GraphAlignmentViewer. Specifically, the EH output has exactly one extra repeat element for all alleles. Is this a known issue, and if so is there a workaround? EH input variant catalog, output json, and output GraphAlignmentViewer attached.


test_output_MGL2.json
test_variant.json