Contig header and Chrom record order do not match reference order

Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF

Apache License 2.0

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Contig header and Chrom record order do not match reference order #28

Closed brmyers closed 5 years ago

brmyers commented 5 years ago

Something I'm altering with post-processing, but it'd be nice if the contig order matched the reference given. In my example, the reference is 1-22,X,Y,MT and the program writes contig headers and records as 1-22,MT, X,Y.

If the reference order was maintained I think that would obviate concerns about "human specific" sorting in code.

Thanks!

KelleyRyanM commented 5 years ago

Candidate implementation of this is available in branch https://github.com/Illumina/GTCtoVCF/tree/python3_compatibility, currently open pull request at https://github.com/Illumina/GTCtoVCF/pull/30.