Updating MarkDuplicatesSpark tiebreaking to reflect changes in picard #5011
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 Report
@@ Coverage Diff @@
## master #5011 +/- ##
================================================
+ Coverage 60.157% 86.078% +25.921%
- Complexity 12768 29356 +16588
================================================
Files 1095 1783 +688
Lines 64608 134963 +70355
Branches 10395 15463 +5068
================================================
+ Hits 38866 116173 +77307
+ Misses 21504 13350 -8154
- Partials 4238 5440 +1202
|
lbergelson
approved these changes
Jul 18, 2018
There was a problem hiding this comment.
@jamesemery Documentation comments. Looks good otherwise. Do you have any sense if the short circuiting for single pairs saves us any time?
| import picard.sam.util.PhysicalLocation; | ||
|
|
||
| /** | ||
| * A common interface for holding the fields in PhysicalLocation |
|
|
||
| // Methods for OpticalDuplicateFinder.PhysicalLocation | ||
| @Override | ||
| public short getReadGroup() { return this.readGroupIndex; } |
There was a problem hiding this comment.
it's weird that these read group isn't transient but the others are, should you javadoc that?
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Outdated suggestions cannot be applied.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.
Tests ported from picard: broadinstitute/picard#1195
Fixes #4707