Changed FilterIntervals to operate on the intersection of intervals in all inputs. #5408
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samuelklee
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@@ Coverage Diff @@
## master #5408 +/- ##
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- Coverage 87.07% 87.069% -0.001%
- Complexity 31244 31249 +5
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Files 1922 1922
Lines 144210 144262 +52
Branches 15916 15916
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+ Hits 125564 125608 +44
- Misses 12872 12881 +9
+ Partials 5774 5773 -1
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| final File firstReadCountFile = inputReadCountFiles.get(0); | ||
| final SimpleCountCollection firstReadCounts = SimpleCountCollection.read(firstReadCountFile); | ||
| metadata = firstReadCounts.getMetadata(); | ||
| resolved = intervalArgumentCollection.getIntervals(metadata.getSequenceDictionary()); |
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Maybe check that the sequence dictionary is the same in counts file and intervals file?
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The intervals file may not have a sequence dictionary (e.g., we can just pass intervals as strings from the command line). This code takes the sequence dictionary from the first read count file, which is used to check other inputs. Probably we should check for the presence of a master dictionary, which may come from the intervals---let me try that.
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Hmm, actually it looks like checking interval files for a sequence dictionary would require a bit of extra code. (Even getBestAvailableSequenceDictionary in GATKTool has a TODO for this.) Will punt for the time being.
| countFiles, lowCountFilterCountThreshold, percentageOfSamples, 1., 99., percentageOfSamples, | ||
| IntStream.range(numIntervalsBelowCountThreshold + 1, numIntervalsBelowCountThreshold + 99).boxed().collect(Collectors.toList())}, | ||
| {intervalsFile, annotatedIntervalsFile, 0.1, 0.9, 0.1, 0.9, 0.1, 0.9, | ||
| {intervalsFile, Collections.emptyList(), annotatedIntervalsFile, 0.1, 0.9, 0.1, 0.9, 0.1, 0.9, |
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It would be nice to have a test case where the annotatedIntervalsFile and countFiles is missing a few entries, up to you!
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OK, added a few simple tests where the -L intervals have an extra interval that should be dropped. Didn't add tests to check for the intersection of annotated intervals, count intervals, and -L intervals, though...
samuelklee
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Thanks @asmirnov239, will merge once tests pass unless you have further objections! |
Closes #5388.