ANGSD: Analysis of next generation Sequencing Data

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User:Thorfinn: Difference between revisions

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# fix wiki doc with -sites should contain -rf with curs from -sites
# fix wiki doc with -sites should contain -rf with curs from -sites
#describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
# from morten shitoutput  
# from morten shitoutput  
<pre>
h1 h2 h3 = 7 10 5  has less than 3 blocks. skipping
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 = 8 10 5  has less than 3 blocks. skipping
Line 30: Line 30:
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1 h2 h3 = 9 10 6  has less than 3 blocks. skipping
h1…
h1…
 
</pre>
# fix -doFasta for single chromosomes. put gzwrite && bufstr.l =0 whenever we change cur
# fix -doFasta for single chromosomes.  


#-doMaf 4 is not working if post is not external
#-doMaf 4 is not working if post is not external
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# better screen output if unsorted filtering
# better screen output if unsorted filtering
=addtional method=
=addtional method=
# make haploid 1dsfs
# make haploid 1dsfs

Revision as of 16:24, 5 March 2014

Wiki doc

  1. write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
  2. -sites does not work without all chromsomes being in the *sites file
  3. user custom class missing

Code fix

  1. -samglfclean not documented
  1. soap usage is not documented


  1. -sites does not work without all chromsomes being in the *sites file
  2. -sites gives wrong chromomosome in error



  1. fix wiki doc with -sites should contain -rf with curs from -sites
  2. 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. fix -doFasta for single chromosomes.
  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 method

  1. make haploid 1dsfs