SMaSH does not evaluate compound het variants correctly

[jn80842]

SMaSH doesn't evaluate compound heterozygous variants correctly (phased or unphased).

true.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 20332447 . C T 20 PASS . GT 0/1
chr13 20332452 . CA C 20 PASS . GT 0/1

pred.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 20332447 . CGTCTCA TGTCTCA,CGTCTC 20 PASS . GT 1/2

Evaluates to two false negatives and one false positive.