adding new ReadQueryNameComparator #4731
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lbergelson
commented
May 2, 2018
lbergelson
commented
- this should match the results of SAMRecordQueryNameComparator exactly
- it operates on GATKRead instead of SAMRecord
* this should match the results of SAMRecordQueryNameComparator exactly * it operates on GATKRead instead of SAMRecord
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| @Test(dataProvider = "getReads") | ||
| public void testTieBreakers(GATKRead left, GATKRead right){ |
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this looks like a much cleaner approach than the equivalent approach in ReadsCoordinateComparator
Codecov Report
@@ Coverage Diff @@
## master #4731 +/- ##
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+ Coverage 79.977% 79.992% +0.015%
- Complexity 17397 17421 +24
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Files 1080 1081 +1
Lines 63093 63119 +26
Branches 10179 10195 +16
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+ Hits 50460 50490 +30
+ Misses 8648 8644 -4
Partials 3985 3985
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| /** | ||
| * compare {@link GATKRead} by queryname | ||
| * duplicates the exact ordering of {@link SAMRecordQueryNameComparator} |
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Duplication of code from HTSJDK to GATK (and other downstream projects) is a sign that htsjdk needs to evolve to an interface-based - as @lbergelson is a maintainer, I point out again that #4340 and htsjdk-related issues should be a high priority!
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@magicDGS You're very right. We had hoped to begin work on a major htsjdk revamp last quarter, but we didn't have enough bandwidth to take it on along with other requirements we had. We're hoping to start very soon.
* added a new queryname comparator for GATKRead it operates on GATKRead instead of SAMRecord * this matches the results of SAMRecordQueryNameComparator exactly
