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ref sequence order enhancements #1007

merged 9 commits into from Feb 27, 2018


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rbuels commented Feb 26, 2018

adds --noSort option to that preserves the order of the input sequence file.

adds support for a by_list value for refSeqOrder in the tracks.conf, which allows people to manually specify the order of their reference sequences

fixes #925 and #919

@rbuels rbuels added the feature req label Feb 26, 2018

@rbuels rbuels added this to the 1.12.5 milestone Feb 26, 2018

@rbuels rbuels self-assigned this Feb 26, 2018

@rbuels rbuels requested a review from cmdcolin Feb 26, 2018

@wafflebot wafflebot bot added the in progress label Feb 26, 2018

@rbuels rbuels requested a review from rdhayes Feb 26, 2018


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cmdcolin commented Feb 26, 2018

Looks good to me :) tested noSort option and the refSeqOrderList override. and they both work.

I guess I'm wondering, if refSeqOrderList exists, can we just get rid of manually setting refSeqOrder: "by_list"?

@rbuels rbuels merged commit 4cf41b7 into dev Feb 27, 2018

@wafflebot wafflebot bot removed the in progress label Feb 27, 2018

@rbuels rbuels deleted the refseqorder branch Feb 28, 2018

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