Older version of dmd not happy with unqualified parameters
Merge branch 'master' of git://github.com/kbroman/qtlHD into karl
CLI: handling options
Rakefile: rake run invoktes test of scanone CLI
Rakefile: included qtab_read_files twice
Qtab: autodetection
Remove exception from gels() for linear regression with matrix of full rank

  - In calc_linreg_rss_fullrank, I switch to dgelsy if dgels didn't
    work, so I shouldn't throw an exception in gels().

  - Also removed some trailing whitespace
Re-write get_peak_scanone

  - Doing a sort was overkill
  - Now if there are multiple positions with the same LOD score, it returns a random
    position from among them
Add to unit test of get_peak_scanone

 - Include case with multiple positions sharing the maximum LOD score
Move create_scanone_Xmatrix to util.d (formerly peaks.d)
Add functions to count founder alleles
Collapse genotype probs to allele probs
Alt version of collapse_geno_prob_to_allele_prob

  - version taking vector of true genotypes and then calculating allele
    frequency table, and then one with the allele freq table
    pre-calculated

  - the latter (allele freq table pre-calculated) allows flexibility
    to first collapse to diallelic QTL model
Cosmetic change
Add test of scanone with additive allele model
Merge branch 'master' of git://github.com/kbroman/qtlHD
Qtab: autodetect symbol file
qtab: autodetect
qtab: document founder/sex support
Qtab doc: support for directional founders