Simplify BedToIntervalList by not reimplementing coordinate conversion #1292
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* BedToIntervalList spends a lot of comments complaining about coordinate conversions after explicitely setting the codec to not perform the conversion from [0,..) to [1,..] * Simplified by just using the baked in conversion instead of disabling it.
| * so it returns 1-based starts. Ugh. Set to zero. | ||
| */ | ||
| final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false); | ||
| final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(), false); |
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will this be able to read a bed that has position 0?
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(the tests are not very good...they just test that the dictionary is right and that the program didn't crash...)
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Good question.. The tests do actually test the output interval see testBedToIntervalListDataProvider, that's how we noticed that there was a bug with merging 0-length intervals.
With some experimentation: 0 intervals that start at 0 work, 0-length intervals that start as 0 have never worked... I added a fix and a new test.
To be complete we might want to allow the weird edge case of the zero-length interval AFTER the end of the contig... My guess is that doesn't work either... GATK will almost certainly explode if it sees one of those as well.
#1292) * Simplify BedToIntervalList by not reimplementing coordiant conversion * BedToIntervalList spends a lot of comments complaining about coordinate conversions after explicitely setting the codec to not perform the conversion from [0,..) to [1,..] * Simplified by just using the baked in conversion instead of disabling it. * add more tests and fix for zero-length edge case at the start of the contig
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Maybe I'm missing something clever that it's doing here...
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