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Sequence dictionary records in TwoBitFile are not stable #1502

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tomwhite opened this Issue Apr 24, 2017 · 2 comments

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tomwhite commented Apr 24, 2017

The order of the contigs in a dictionary produced from TwoBitFile is not the same as the order they are stored in in the .2bit file.

I think the problem is the records are being stored in a standard map, rather than one that preserves insertion order (like ListMap).

See https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala#L70

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heuermh Apr 24, 2017

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Good catch! In what applications would the order matter?

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heuermh commented Apr 24, 2017

Good catch! In what applications would the order matter?

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I had some problems with partitioning in GATK which boiled down to the ordering of the reference sequence dictionary. I think a fasta dict file has an order, so it would be good to be consistent with that if possible.

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tomwhite commented Apr 24, 2017

I had some problems with partitioning in GATK which boiled down to the ordering of the reference sequence dictionary. I think a fasta dict file has an order, so it would be good to be consistent with that if possible.

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