User:Thorfinn

1. Thetas,Tajima,Neutrality test needs documentation and examples files

1. doMajorMinor 4 fjerner sites som ikke har major/minor som ref. total maerkeligt og fucked up
2. user custom class missing

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. phat does not work alone (-doMaf 8)

1. make haploid 1dsfs
2. fix wiki doc with -sites should contain -rf with curs from -sites
3. describe -trim! does trim 3 remove the first and last 3 bases? or just 2?
4. 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. put gzwrite && bufstr.l =0 whenever we change cur

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

Anders changes to version 583

1) Default minMaf set to -1 (instead of 0)

2) added

 freqs->freq = new double[pars->numSites]; 

to phatLoop

added the if part of if(freq->freq==NULL)

 freq->freq = new double[pars->numSites]; 

to postFreq and likeFreq funcitons to stop leak + be able to run phat without postFreq/likeFreq

3) changed doMajorMinor 2 to choose a minor allele even if no minor allele is observed (if -minMaf is chosen the site will be removed). This avoid removing side through the majorMinorMod function. The change else if (bases[i]>temp){ -> else if (bases[i]>=temp){ in majorMinorCounts

4) Estimate nInd even if -minInd 0. Else the output is wrong when -minInd 0 filter::run changed

e.g.

$ANG -out out -doMajorMinor 2 -doMaf 8 -bam bam.filelist -doCounts 1 -r 1: before gunzip -c out.mafs.gz | headchromo position major minor phat nInd

1 13999919 A T 0.000000 10

1 13999920 G T 0.000000 10

1 13999921 G T 0.000000 10

1 13999922 C T 0.000000 10

after chromo position major minor phat nInd

1 13999919 A T 0.000000 1

1 13999920 G T 0.000000 1

1 13999921 G T 0.000000 1

1 13999922 C T 0.000000 1

1 13999923 A T 0.000000 1

(there is only information for one individual)