User:Thorfinn

ms stuff

./msHOT-lite 2 20 -t 30000 -r 6000 30000000 -eN 0.01 0.1 -eN 0.06 1 -eN 0.2 0.5 -eN 1 1 -eN 2 2 -l

N0=theta/regionsize/4*u

30000.0/30000000.0/4.0/u=10000

Wiki doc

1. check userdir is writable
2. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
3. user custom class missing

Code fix/cleanup

1. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor tsk 7april ?
2. don't quit program if a chr is not included in the -sites file
3. check all getoptions stderr output.
4. from morten shitoutput

h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 11 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 12 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 13 5  has less than 3 blocks. skipping
h1 h2 h3 = 10 15 5  has less than 3 blocks. skipping
h1 h2 h3 = 7 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 8 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…

Addtional methods and functionality

1. make haploid 1dsfs
2. simplefy filereading. from glf files
3. fix -doFasta for single chromosomes.