Negative length in GeneModelGenerationService.determineGeneFeatures

[jchriste-jcvi]

With master@96585d

java.lang.IllegalArgumentException: length can not be negative at org.jcvi.jillion.core.Range$Builder.assertValidCoordinates(Range.java:2856) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.service.GeneModelGenerationService.determineGeneFeatures(GeneModelGenerationService.java:394) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.service.GeneModelGenerationService.generateGeneModel(GeneModelGenerationService.java:57) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.generateGeneModels(Vigor.java:398) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.modelsFromNucleotideRecord(Vigor.java:300) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.generateAnnotations(Vigor.java:243) ~[vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.Vigor.run(Vigor.java:90) [vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?] at org.jcvi.vigor.Application.main(Application.java:12) [vigor-4.1.20200430-192814-96585d9-jar-with-dependencies.jar:?]

[dkatzel-ncats]

is this a range for a gene that is in the opposite direction? Jillion does have a DirectedRange if you mean the stop is before the start coordinate

[jchriste-jcvi]

Stalker!

[jchriste-jcvi]

I haven't looked into it, but when I encountered it before it was just an error. We tried to make the code work in the forward direction while keeping a note of which strand it was on. It was simpler for adding the reverse strand case which most of the code hadn't been accounting for. I'll let you know.

[jchriste-jcvi]

fixed with 208d48f. It was caused by misordering the exons, followed by assuming an ordered list.