Bugs

1. check numSites==0 in all generals: derived classes.

2. check if subdirs exists in outputfiles. Otherwise subtle crash.

3. Only print the

If you have selected more than one MAF estimator we will choose in following order
   1. knownminor bfgs
   2. knownminor EM
   3. unknownminor bfgs
   4. unknownminor EM
   5. Posterior maf

If use has selected multple mafs estimators.

4. write about single bam -i on wiki

5. fix the maxsize of a chr now its 270e6 Best

6.

when you do doPost without doMaf gives SEGfault

7.

use std::isnan std::isinf instead of isnan/isinf such that things work for macos. when tou do doGeno 2 all the non variable genotypes appear as 2

8.

For dumping beaglestyle output you need to estimate major/minor: -doMajorMinor ./angsd -bam /home/tspr/filelist -GL 1 -r chr8:12500000 -out results -doGlf 4

9.

nice screen informaqtion doesan't work for /home/software/angsd/angsd0.4471/angsd -doGlf

10.

Huge problem -doSNP only works if -doMAf is included.

11.

Combination of minmapq causes alle 10llh for all samples to be zero. so keeplist is now modified in analysisEstLikst.cpp

12. implement rg groups,

13

should rna be implemented

14

fix the filter input. bed file bim file. etc.

15. offset in hwe printout is wrong

16. plug in the hwe estimate into the .mafs file

17. another thing, don't know why but HWE at some sites gives F = nan I'm currently just ignoring these sites but just to let you know.

18. combination of -r/-rf is only testing first bamfile if data exists. This can be pretty serious.

FGV

Thorfinn