v1.3.0

20MAY2020 - selscan v1.3.0 - Log ratios are now output as log10 not natural logs (beware comparisons with raw selscan computations from versions prior to v1.3.0). New statistics implemented.

--pmap <bool>: Set this flag to use physical distance instead of genetic map

Introduction of XP-nSL, this statistic is a cross population statistic for identifying hard/soft sweeps. Does not require a genetic map. XP-nSL:nSL::XP-EHH:iHS. Cite ZA Szpiech et al. (2020) High-altitude adaptation in rhesus macaques. bioRxiv doi: https://doi.org/10.1101/2020.05.19.104380

--xpnsl <bool>: Set this flag to calculate XP-nSL.
Default: false

Normalize XP-nSL with --xpnsl flag in norm.

lasugden adds the option to calculate XP-EHH with either definition of EHH. By default, uses original denominator (N choose 2). To use denominator defined in Wagh et al. for better performance on incomplete sweeps, use flag --wagh

--wagh <bool>: Set this flag to calculate EHH with Wagh denominator. For xpehh only. DO NOT use with --alt
Default: false

Normalize these computations with --xpehh flag in norm.

norm v1.3.0 - Now supports --xpnsl flag, which is identical to using --xpehh.
--qbins now has a default value of 10 instead of 20.
--bp-win analyses have been changed when analyzing XP-EHH and XP-nSL scores. Since positive scores suggest adaptation in the first (non-ref) population and negative scores suggest adaptation in the second (ref) population, we split windows into those enriched for extreme positive scores and those enriched for extreme negative scores.
min and max scores are given for each window for XP statistics, and the max |score| is reported for iHS and nSL stats.

*.windows output files therefore have additional columns:

For XP stats:
<# scores in win>

For iHS and nSL:
<# scores in win>