Simwalk2 haplotyping run input files (TABLE*.ALL and HAPLO*.*).
An optional parameter (-a) specifies that all haplotype estimates
should be considered. The default is to ignore haplotype vectors
that simwalk2 has marked as candidates for re-analysis. (This
reanalysis can be carried out by copying the RERUN-NN.BCH file
into BATCH2.DAT and rerunning simwalk2).
