Cannot merge tabix files with different sequence names #108
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It would be good to merge this soon as it fixes an a bug that comes up a lot in practice. There are follow-on changes for htsjdk (as usual) that I'll propose upstream. |
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I've incorporated the htsjdk parts of this in samtools/htsjdk#1263. I'd like to merge this soon unless there are any objections. |
heuermh
approved these changes
Jun 24, 2019
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I suggest either rebase + squash + force push or use Squash and merge button to merge commits. |
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Thanks for approving @heuermh |
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Fixes broadinstitute/gatk#5997.
Each
TabixIndexonly stores the sequence names for the sequences it sees, which is a problem when merging indexes for the part files. So if one part only seeschr1it will only have that in its list, while if another seeschr2andchr3it will have those in its list. The issue occurs since the reference index is used, so for the first part 0 would bechr1, whereas for the second it would bechr2. The solution is to store content for all sequences from the header (even if for that part the conent is null for a given sequence), which is what this change does.