Add support for multi-allelic variants #976
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## tb-add-downsample-vcf #976 +/- ##
=========================================================
- Coverage 95.64% 95.63% -0.01%
=========================================================
Files 127 127
Lines 7457 7473 +16
Branches 521 501 -20
=========================================================
+ Hits 7132 7147 +15
- Misses 325 326 +1
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
jdidion
force-pushed
the
multiallelic-likelihoods
branch
from
f559b3f
to
87f07fe
Compare
jdidion
force-pushed
the
multiallelic-likelihoods
branch
from
87f07fe
to
8f7a4eb
Compare
TedBrookings
approved these changes
Apr 12, 2024
Comment on lines
+146
to
+159
| val logProbs: Array[Double] = Array( | ||
| math.log10(epsilon), | ||
| math.log10((1 - epsilon) / 2), | ||
| math.log10(1 - epsilon) | ||
| ) | ||
| // compute genotype log-likelihoods | ||
| (0 until numAlleles).flatMap(b => | ||
| (0 to b).map(a => | ||
| (0 until numAlleles).map(allele => | ||
| logProbs(Array(a, b).count(_ == allele)) * alleleDepths(allele) | ||
| ).sum | ||
| ) | ||
| ) | ||
| } |
There was a problem hiding this comment.
I see that this passes the equivalency test with the biallelic case, but I found it very difficult to understand. It might help to have a bit more commentary here. I'd suggest at least something like:
// compute genotype log-likelihoods in a flat array pairing each allele with all alleles earlier or equal to it
// e.g. lp_AA, lp_BA, lp_BB, lp_CA, lp_CB, lp_CC, ...
| Likelihoods.logToPhredLikelihoods(genotypeLikelihoods) | ||
| } | ||
|
|
||
| def mostLikelyGenotype: Option[(Int, Int)] = { |
There was a problem hiding this comment.
Suggested change
| def mostLikelyGenotype: Option[(Int, Int)] = { | |
| private def mostLikelyGenotype: Option[(Int, Int)] = { |
| @@ -13,6 +13,7 @@ import com.fulcrumgenomics.vcf.DownsampleVcf.{downsampleAndRegenotype, winnowVar | |||
|
|
|||
| import scala.math.log10 | |||
| import scala.util.Random | |||
| import scala.tools.nsc.doc.html.HtmlTags | |||
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.