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. fix ./angsd0.591.smartcount/angsd -i angsd0.591.smartcount/DNK02.hg19.flt.sort.rmdup.realign.md.bam -out tmp -minQ 20 -minMapQ 30 -P 2 does nothing but crashes
2. check that first line in .arg file is the command used
3. check domajorminor for -domaf complains about it lagging
4. fix -r problem if chromosome contains :
5. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
6. don't quit program if a chr is not included in the -sites file
7. check all getoptions stderr output.
8. -samglfclean not documented
9. soap usage is not documented
10. 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.