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Original qualities are parsed out, but left in attribute fields #483

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fnothaft opened this Issue Nov 17, 2014 · 2 comments

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fnothaft commented Nov 17, 2014

Not sure whether to call this a bug or not... When we convert from BAM, we parse the original qualities field out into the ADAM format, but we don't remove this from the attributes tag string. I have a suspicion that we do the same thing for all tags (e.g., OP, OC, MD)... For files with OC for example, this leads to a 25% penalty in size on disk.

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fnothaft Feb 23, 2015

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@Ibracadabra05 will be tackling this.

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fnothaft commented Feb 23, 2015

@Ibracadabra05 will be tackling this.

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Ibracadabra05 commented Feb 24, 2015

Roger that.

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 17, 2016

[ADAM-483] Properly handle denormalized OP, OC, OQ fields.
Properly splits the denormalized fields out of the attribute line. Adds better
test coverage to SAMRecordConverterSuite. Oddly enough, the other side of the
conversion (AlignmentRecordConverterSuite) had coverage. Resolves #483.

@heuermh heuermh closed this in 5dd13b9 Jul 19, 2016

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