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Rename Contig objects #43

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fnothaft opened this issue Feb 9, 2015 · 2 comments
Closed

Rename Contig objects #43

fnothaft opened this issue Feb 9, 2015 · 2 comments
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@fnothaft
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enhancement
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0.12.0

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@fnothaft
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fnothaft commented Feb 9, 2015

I was writing code that munged NucleotideContigFragments and realized that Contig should be changed to Reference and NucleotideContigFragment should be renamed to Contig or ContigFragment.
@fnothaft fnothaft self-assigned this Feb 9, 2015
@laserson
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+1

@heuermh
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heuermh commented May 20, 2016

Consider also the renaming proposal in bigdatagenomics/adam#997.

Perhaps

Contig -> Reference
new schema class ReferenceSet (or References, or Assembly, or SequenceDictionary, or ?)
new schema class Sequence
new schema class or enum Alphabet
NucleotideContigFragment -> SequenceFragment (or SequencePartition, or Slice, or ?)

@fnothaft fnothaft mentioned this issue Mar 2, 2017
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@heuermh heuermh modified the milestone: 0.12.0 May 23, 2017
@heuermh heuermh mentioned this issue Oct 11, 2017
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@heuermh heuermh mentioned this issue Dec 11, 2018
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