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. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
2. don't quit program if a chr is not included in the -sites file
3. check all getoptions stderr output.
4. -samglfclean not documented
5. soap usage is not documented
6. 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…

fix alignement of output

	-> [analysisKeepList.cpp] -sites is still beta, use at own risk...
Filter file contains major/minor information to use these in analysis supper '-doMajorMinor 3'
	-> Reading fasta: /space/genomes/refgenomes/hg19/gatk/hg19.fa
Will call genotypes using sample allele frequencies
	-> Parsing 33 number of samples 
	-> Printing at chr: 1 pos:566303 chunknumber 1800Segmentation fault (core dumped)

Addtional methods and functionality

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