Calculate nSL plus option for more detailed output for iHS

15JUNE2015 - Release of 1.1.0. tomkinsc adds the --ihs-detail parameter which, when provided as an adjunct to --ihs, will cause selscan to write out four additional columns to the output file of iHS calculations (in order): derived_ihh_left, derived_ihh_right, ancestral_ihh_left, and ancestral_ihh_right.

An example file row follows, with header added for clarity.

locus phys-pos 1_freq ihh_1 ihh_0 ihs derived_ihh_left derived_ihh_right ancestral_ihh_left ancestral_ihh_right

16133705 16133705 0.873626 0.0961264 0.105545 -0.0934761 0.0505176 0.0456087 0.0539295 0.0516158

From these values we can calculate iHS, but it is preserved in the output for convenience. Having left and right integral information may assist certain machine learning models that gain information from iHH asymmetry.

selscan can now calculate the nSL statistic described in A Ferrer-Admetlla, et al. (2014) MBE, 31: 1275-1291. Also introduced a check on map distance ordering. Three new command line options.

--nsl : Set this flag to calculate nSL.
Default: false

--max-extend-nsl : The maximum distance an nSL haplotype is allowed to extend from the core.
Set <= 0 for no restriction.
Default: 100

--ihs-detail : Set this flag to write out left and right iHH scores for '1' and '0' in addition to iHS.