PyVCF
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is_deletion property fails for _SingleBreakend
when self.is_deletion is invoked for this type of record, a TypeError is thrown
-> if len(self.REF) > len(alt_allele):
(Pdb) l
439 if self.is_indel:
440 # just one alt allele
441 alt_allele = self.ALT[0]
442 if alt_allele is None:
443 return True
444 -> if len(self.REF) > len(alt_allele):
445 return True
446 else:
447 return False
448 else:
449 return False
(Pdb) self.ALT
[T.]
(Pdb) self.REF
'TGCCGCCAGCCCCCCGG'
(Pdb) len(self.ALT)
1
(Pdb) len(alt_allele)
*** TypeError: object of type '_SingleBreakend' has no len()
Should return TRUE.