New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Kt fingerprintchecker fix #596
Conversation
@@ -151,8 +147,8 @@ public void setpLossofHet(final double pLossofHet) { | |||
if (samples == null) samples = ctx.getSampleNames(); | |||
|
|||
if (isUsableSnp(ctx)) { | |||
final HaplotypeBlock h = this.haplotypes.getHaplotype(ctx.getChr(), ctx.getStart()); | |||
final Snp snp = this.haplotypes.getSnp(ctx.getChr(), ctx.getStart()); | |||
final HaplotypeBlock h = this.haplotypes.getHaplotype(ctx.getContig(), ctx.getStart()); |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
why is this changing?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
getChr
is deprecated?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@jsotobroad @nh13 The method getChr() is depreciated along and it was changed along all classes that use it. It simply wasn't changed yet to match its original form to make sure the replacement of GenotypeReader wasn't hindered by it. I changed it after looking deeper into getChr() which only calls getContig() so no error would have occurred anyway.
👍 |
No description provided.