Loop breaking and Mendel output file bugs

[Nandita Mukhopadhyay]

1) The loop-breaking function was implemented to select as loop-breakers individuals who were maximally genotyped, but doesn't do this any more. Why? Because it fails to actually count the genotypes, as I discovered while debugging; the number of loci it loops over is 0! Any help would be greatly helpful, as I am attempting to go through several large and terribly complex pedigrees. Otherwise I will have to fall back on makeped, and select loop-breakers manually.

2) The Mendel (new) output option fails to handle pedigrees that have IDs like 12345678-12345678. The individual ID is not filled in.

Thanks for any suggestions.

Nandita

[Nandita Mukhopadhyay]

Correction re item 2) above: in the Mendel option, the locus file names both alleles "2", for mono-alleleic SNPs.
Sorry for the confusion. Regards, Nandita