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Add pathA##idx##pathB support for CRAM indices. #1360

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merged 1 commit into from
Nov 18, 2021

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jkbonfield
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Fixes samtools/samtools#1541

The original report was for s3: URIs, but it turns out this is simply lacking in local files too. It seems surprising we never implemented this, but even in 1.10 (where ##idx## was first added) CRAM support was missing. 7e583cc stated "it works transparently for all file types and all programs". I guess we never actually checked it.

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Note given it was just hts_idx_load that had this functionality, and now it's also cram_index_load, my guess is "all formats" still isn't true as we have other index types such as gzi (and maybe tbi) which aren't part of the standard index formats. I think they're substantially less common though.

@daviesrob daviesrob merged commit f1ac6bb into samtools:develop Nov 18, 2021
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inconsistent support for ##idx## remote urls between BAM & CRAM
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