"detect_cnv.pl -validate" shows probability instead of state

[heliac2000]

$ runexpl --path_detect_cnv=../detect_cnv.pl 5

ex5.rawcnv:
chr3:3957986-4054960          numsnp=50     length=96,975      state86.4199950337373,cn=84.4199950337373 father.txt startsnp=rs11716390 endsnp=rs17039742
chr20:10511631-10583260       numsnp=10     length=71,630      state11.5231778900509,cn=9.5231778900509 father.txt startsnp=rs8114269 endsnp=rs682562

state and cn have strange values...

#assign the score for each region (similar to assignConfidence subroutine)
sub validateRegion {
                       :
  for my $nextstate (1, 2, 3, 5, 6) {   #do not consider LOH
                       :
    push @logprob, [$logprob + log ($prior_prob->[$stateindex]), $nextstate];
                       : 
  }
                       :
  @logprob = sort {$b->[0]<=>$a->[0]} @logprob;
  my $beststate = $logprob[0]->[0];

$logprob[0]->[0](probability) is assgined to $beststate, but a state value($logprob[0]->[1]) should be assigned.

  my $beststate = $logprob[0]->[1];

I try to rerun, outputs changed as follows.

chr20:10511631-10583260       numsnp=10     length=71,630      state2,cn=1 father.txt startsnp=rs8114269 endsnp=rs682562
chr3:3957986-4054960          numsnp=50     length=96,975      state2,cn=1 offspring.txt startsnp=rs11716390 endsnp=rs17039742

[jeffverboon]

same issue!

[kaichop]

we will review this and revise.

On Sat, May 26, 2018 at 2:37 PM, jeffverboon notifications@github.com wrote:

same issue!

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[fangli80]

Thank you. We have fixed it.