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
- user custom class missing
- -samglfclean not documented
- soap usage is not documented
- -sites does not work without all chromsomes being in the *sites file
- -sites gives wrong chromomosome in error
- phat does not work alone (-doMaf 8)
- make haploid 1dsfs
- 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
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 -doFasta for single chromosomes. put gzwrite && bufstr.l =0 whenever we change chr