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EVA-1665 VCF headers list the contigs in accession order #172

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EVA-1665 VCF headers list the contigs in accession order #172

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Commits on Sep 13, 2019

  1. use system sort for the list of contigs 

    Of course this is platform dependent, but given that we have some
species with lots of contigs (e.g. almost 0.5M for rat or turkey),
we can either:

- keep the hacky implementation of this commit.
- evaluate memory performance of: loading the file into
a list, sort the list in memory, write the list. For at least a
couple million of 20 bytes strings.

If we go for the second option, the changes have to be done in the
same place as the current system sort.
    @jmmut
    jmmut committed Sep 13, 2019
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Commits on Sep 16, 2019

  1. add test for contig order

    @andresfsilva
    andresfsilva committed Sep 16, 2019
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  2. write the contig file in order

    @andresfsilva
    andresfsilva committed Sep 16, 2019
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