dragmap

[ewels]

Quoting @dslarm :

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bunch of x86 specific compile flags, and also use of x86 intrinsics. Any volunteers? There’s a simple #include that will solve this (as per bwa-mem2 and hisat2)

@maxulysse
Note that the latest dragmap is not working, which is why we patched it to an older version in sarek

so we use dragmap=1.2.1 + samtools=1.19.2 and pigz=2.3.4

[delagoya]

repo at https://github.com/Illumina/DRAGMAP

[lrbison]

I have a DRAGMAP build from source working on arm64 now. Working on testing to make sure I didn't disable anything on x86 either.

One odd thing is that I cannot see DRAGMAP in bioconda on my arm instance at all. Must need some additional recipe configuration (https://bioconda.github.io/recipes/dragmap/README.html)

One concern is https://github.com/Illumina/DRAGMAP/blob/master/thirdparty/dragen/src/common/hash_generation/hash_table.c#L2223 but it seems that the atomic updates should do the synchronization without additional asm sections.

[lrbison]

PR to DRAGMAP based on master is up: Illumina/DRAGMAP#65
Although according to their page, they are not accepting PRs. We'll have to pull in a patch.

My PR doesn't cleanly backport to dragmap=1.2.1. I will make another if necessary.

[delagoya]

Nice. I am looking into how we can get the PR reviewed and accepted by DRAGEN team.

[dslarm]

@delagoya , @lrbison , @ewels - came to conclusion that dragmap was optional, lightly used, and so not required. dropped priority to low.