validatevariants -gvcf fix #3530
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added 2 commits
August 28, 2017 17:24
…s followed by a record that the previous one fully encompasses. The interval math was off in this case
Codecov Report
@@ Coverage Diff @@
## master #3530 +/- ##
==============================================
+ Coverage 80.079% 80.109% +0.03%
- Complexity 17760 17791 +31
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Files 1188 1188
Lines 64410 64543 +133
Branches 10004 10022 +18
==============================================
+ Hits 51579 51705 +126
Misses 8845 8845
- Partials 3986 3993 +7
|
yfarjoun
approved these changes
Aug 29, 2017
| @@ -205,10 +205,13 @@ public void apply(final VariantContext vc, final ReadsContext readsContext, fina | |||
| // if the current record is adjacent to the previous record and "overlap" them if they are so our set is as | |||
| // small as possible while still containing the same bases. | |||
| final int start = (previousInterval != null && previousInterval.overlapsWithMargin(refInterval, 1)) ? | |||
| previousInterval.getEnd() : refInterval.getStart(); | |||
| genomeLocSortedSet.add(genomeLocSortedSet.getGenomeLocParser().createGenomeLoc(refInterval.getContig(), start, vc.getEnd()), true); | |||
| Math.min(previousInterval.getStart(), refInterval.getStart()) : refInterval.getStart(); | |||
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will this:
Math.min(previousInterval.getStart(), refInterval.getStart())
not always equal previousInterval.getStart() given the order of iteration?
|
@lbergelson fix for an incorrect assumption I had made previously, if you or someone else could review thanks! |
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fix issue with validatevariants when validatign a gvcf and a record is followed by a record that is fully encompassed by the first one. The interval math was off in this case