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add prepare-refseqs.pl --unsorted to preserve fasta sequence order #924

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@dsenalik
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commented Sep 11, 2017

In reference to previous closed issue #867 "Custom Sorting Reference Sequence" and open issue #919 "The refSeqOrder is not customisable", I propose a new parameter to prepare-refseqs.pl of "--unsorted" which will use the sequence order from the input FASTA file or gff file to control the order in the generated json output file. Currently the output is always alphabetically sorted. I have a pull request implementing this new feature (this is my first pull request so be gentle).

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commented Sep 11, 2017

Good idea. Thanks for the pull.

@rbuels rbuels self-assigned this Jan 24, 2018

@rbuels rbuels added this to the 1.12.4 milestone Jan 24, 2018

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commented Jan 25, 2018

We've switched to using this pull request for our JSON builds with success. However, some input fasta files are still not always ordered precisely as we'd like. I have a simple Browser.js patch that adds a "by_list" refSeqOrder option that overrides the default order with config option refSeqOrderList, containing a comma-separated list in desired order.

I think this PR is in a private repo, so I can't check it out and add directly, unless I'm missing something. Attached is a patch file against today's master branch, starting at line 2188...

refSeqOrderList.patch.txt

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commented Jan 25, 2018

These changes (--unsorted and by_list), when landed, will close #925 and #919

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commented Jan 25, 2018

Great! Incorporating this and reconciling with other suggestions. Doing this in the refSeqOrder branch. https://github.com/GMOD/jbrowse/compare/refseqorder

@rbuels rbuels closed this Jan 25, 2018

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