Add documentation of the --only-affected option

Need to add updated examples for the comp_hets analysis output at some point
revert to numpy 1.6.0 to enable OS X custom installations
optmize comp_het loop to avoid n^2
Merge pull request #192 from jxchong/patch-3

Add documentation of the --only-affected option
store sample names and ids as text
tolerate PED files where only one of the two parents is known.
support backwards compatibility