User:Thorfinn

Wiki doc

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

Code fix/cleanup

1. check that first line in .arg file is the command used
2. check domajorminor for -domaf complains about it lagging
3. fix -r problem if chromosome contains :
4. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
5. don't quit program if a chr is not included in the -sites file
6. check all getoptions stderr output.
7. -samglfclean not documented
8. soap usage is not documented
9. 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.