Reproducing TelomereHunter's telomere content

[23Niklas]

Hi, I am trying to reproduce the telomere content estimated for a file from TelomereHunter with qmotif, as shown in your paper (Holmes et al, 2022). It is unclear to me which reads were taken from qmotif to recreate the intratelomeric reads of TelomereHunter. Are these all reads that are output from qmotif, or only the ones with TTAGGG motif, or only the ones with a single base substitution in the motif, or another combination of all the reported motifs? Also unclear to me is how the telomeric reads from qmotif can correspond to the intratelomeric reads from TelomereHunter, since TelomereHunter defines intratelomeric as all telomeric reads that cannot be mapped, whereas qmotif gives exact mappable regions from which the telomeric reads can be extracted through the init file.
I would be very grateful for the answers to my questions, thanks in advance!