Hawk doesn't seem to do Bonferroni correction

[petercombs]

Hi Atif,
I'm running through the pipeline with the Earle bacterial data set to make sure I understand all the steps and what they're doing, and when I get to the runHawk stage, the case_out_w_bonf.kmerDiff and case_out_wo_bonf.kmerDiff have the exact same number of lines:

$ wc -l earle/case_out_w_bonf.kmerDiff
1505783 earle/case_out_w_bonf.kmerDiff
$ wc -l earle/case_out_wo_bonf.kmerDiff
1505783 earle/case_out_wo_bonf.kmerDiff

Any guesses what might be going on here? Thanks!

[atifrahman]

Can you please check what is value of CUTOFF defined in kmer.h? case_out_w_bonf.kmerDiff actually contains k-mers with p-values less than 0.05/CUTOFF. If CUTOFF is very high, all of them will pass Bonferroni correction.

This is from my run on Earle bacterial data set (with default CUTOFF=10,000,000)

ampicillin$ wc -l case_out_wo_bonf.kmerDiff
4778950 case_out_wo_bonf.kmerDiff
ampicillin$ wc -l case_out_w_bonf.kmerDiff
4752738 case_out_w_bonf.kmerDiff

[petercombs]

Looks like it was set to 100,000,000 (I was using commit 1ebe55b). I'm a little confused why you're getting ~3x as many kmers even without bonferroni correction (4.7M instead of 1.5M), which I'll try to track down...