The new chainer could get tricked into attempting to decompose the alleles of a haploid sex chromosome (even though there is only one), so this is a simple filter that removes these phased haplotypes under the assumption that they will consist largely of haploid sequence. The only diploid sequence attached to them should be errors or regions like the PAR.
I also fixed an informatic issue where the boundaries of a bubble could be lost on one haplotype if it was not able to find any alleles through the adjacent bubbles.
The new chainer could get tricked into attempting to decompose the alleles of a haploid sex chromosome (even though there is only one), so this is a simple filter that removes these phased haplotypes under the assumption that they will consist largely of haploid sequence. The only diploid sequence attached to them should be errors or regions like the PAR.
I also fixed an informatic issue where the boundaries of a bubble could be lost on one haplotype if it was not able to find any alleles through the adjacent bubbles.