ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

User:Thorfinn

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Wiki doc

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

Code fix

  1. -samglfclean not documented
  2. soap usage is not documented
  3. fix -doFasta for single chromosomes.
  1. 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…
  1. -doMaf 4 is not working if post is not external
  1. Regarding an open issue of printing %e instead o numbers, using the bombyx/lyca dataset:
  1. fix }else{
   fprintf(stderr,"./a.out [make_bed|do_stat|validate_bed|print]\n");
 }  in thetaStat
  1. simplefy filereading. from glf files
  1. check 1offseted in -sites file
  2. add more info to -sites file output
  1. better screen output if unsorted filtering

addtional methods and functionality

  1. make haploid 1dsfs