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Estimate contig lengths in SequenceDictionary for BED, GFF3, GTF, and NarrowPeak feature formats #1410

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heuermh opened this Issue Mar 1, 2017 · 0 comments

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heuermh commented Mar 1, 2017

For those feature formats that don't have a header we parse (currently BED, GFF3, GTF, NarrowPeak), we could do better than 1L for the contig lengths in the SequenceDictionary

https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala#L109

How about max(f.getStart, f.getEnd) + 1L?

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