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. angsd: angsd_realSFS.cpp:980: void realSFS::algoGeno(int, double**, char*, char*, int, int, kstring_t*, int, int*, int*, double*): Assertion `pest!=__null' failed. this means, ask for -pest if -doSaf 3
2. fix offset in perchunk printout to stderr
3. if(doMajorMinor==4&&refToInt[pars->anc[s]]==4) in analysisMajorMinor
4. don't quit program if a chr is not included in the -sites file
5. check all getoptions stderr output.
6. -samglfclean not documented
7. soap usage is not documented
8. 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)

Problem with command:

./angsd0.585/angsd -sites filt2 -b list -doMajorMinor 4 -doMaf 2 -GL 1 -r 22: -out res9/res22 -doGeno 19 -doPost 1 -doGlf 1 -doSaf 3 -P 6 -pest res1.1/all.saf.em.ml -doCounts 1 -dumpCounts 4 -ref  /space/genomes/refgenomes/hg19/gatk/hg19.fa

-nan | 0.333333 0.333333 0.333333 |1.098612 | 0 | 
[emFrequencyNoFixed] caught nan will exit
w0 0.000000 w1 0.000000 w2 0.000000 

Addtional methods and functionality

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