Revise the REF_PATH / REF_CACHE documentation.#2178
Conversation
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For @daviesrob: one thing you may wish to replace is "If that is done, it is strongly encouraged you also specify a local REF_CACHE The bit about reference sequences and CRAM is incorrect in saying CRAM requires a reference, but I didn't change that text - only punted it lower down in the document. I don't think it's worth getting overly worried about that though as it's how 99.something% of CRAMs are produced. While I think on-the-fly embedded consensus refs are a better solution for many people, they're not really well supported by the archives (I think) and until that happens people will just go with the standard workflow. |
Updates to reflect the changes in the htslib/no-ebi-ref PR. Also moved the section listing the reference discovery ordering to be adjacent to the environment variable section so all relevant text is together.
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Text has been adjusted as requested. Also rebased to avoid unrelated problems with testing that would otherwise occur. |
Ensure it's clear which sub-commands are being referenced Add items for PRs samtools#2178 and samtools#2222 Adjust wording for a couple of items and fix a few typos.
Updates to reflect the changes in the htslib/no-ebi-ref PR.
Also moved the section listing the reference discovery ordering to be adjacent to the environment variable section so all relevant text is together.