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: Difference between revisions
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#user custom class missing | #user custom class missing | ||
=Code fix= | =Code fix= | ||
#-samglfclean not documented | #-samglfclean not documented | ||
#soap usage is not documented | #soap usage is not documented | ||
# fix -doFasta for single chromosomes. | |||
# from morten shitoutput | # from morten shitoutput | ||
<pre> | <pre> | ||
| Line 31: | Line 22: | ||
h1… | h1… | ||
</pre> | </pre> | ||
#-doMaf 4 is not working if post is not external | #-doMaf 4 is not working if post is not external | ||
Revision as of 15:54, 5 March 2014
Wiki doc
- write how on website: Thetas,Tajima,Neutrality test needs documentation and examples files
- -sites does not work without all chromsomes being in the *sites file
- user custom class missing
Code fix
- -samglfclean not documented
- soap usage is not documented
- fix -doFasta for single chromosomes.
- 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…
- -doMaf 4 is not working if post is not external
- Regarding an open issue of printing %e instead o numbers, using the bombyx/lyca dataset:
- fix }else{
fprintf(stderr,"./a.out [make_bed|do_stat|validate_bed|print]\n"); } in thetaStat
- simplefy filereading. from glf files
- check 1offseted in -sites file
- add more info to -sites file output
- better screen output if unsorted filtering
addtional method
- make haploid 1dsfs