Christopher Chang
Christopher Chang
fyi, recent plink 1.9 builds use the SIMDe library (https://github.com/simd-everywhere/simde ) to support ARM builds; see lines 190-195 of the current plink_common.h .
Are you trying to install plink 1.9, 2.0, or both? I know that Debian's plink and plink2 packages support arm64. But if you're on a system without such support, or...
In the current design, the storage-mode (3rd) and header-format byte(s) (usually just the 12th byte, but allowed by the spec to be multibyte) serve this function. (Note that variant-major .bed...
One explicit question raised by the current design is, what happens when the multiallelic-dosage storage format is finalized? I have tried to set things up so that an older pgen...
I am open to making a near-future spec change defining storage-mode 0x11 as "0x10 with a version number", with guarantees on what won't change with each type of version number...
Planning to make the following addition to the specification soon (and release the corresponding plink2 / pgenlibr / Python pgenlib forward-compatibility updates); let me know if you see any problems....
Yes, this will be exposed soon in the C/C++ API.
Specification has been updated. Sample `plink2::SpgwInitPhase1Ex()` call (can be invoked by "--make-pgen writer-ver"): https://github.com/chrchang/plink-ng/commit/dfabcf669d96f4c531a851d43d66f8e50e5fa554#diff-2d7f1e57f1cc7e7dc7a6a9f6f98414c7d839533d0460962aad574e87f0160e82R6474 Sample reading logic (can be invoked by --pgen-info): https://github.com/chrchang/plink-ng/commit/dfabcf669d96f4c531a851d43d66f8e50e5fa554#diff-e3af826ba80b15835975fa856c1081bdd94a6501db99e134ab3f61b4245d43d0R1101 https://github.com/chrchang/plink-ng/commit/dfabcf669d96f4c531a851d43d66f8e50e5fa554#diff-e3af826ba80b15835975fa856c1081bdd94a6501db99e134ab3f61b4245d43d0R1137
The error message means exactly what it says: this feature isn't implemented in plink2 yet. ("Concatenating" merge refers to the "[bcftools concat](http://samtools.github.io/bcftools/bcftools.html#concat)" use case, though plink2's behavior differs a bit...
When two variants share a position, --pmerge-list uses the --sort-vars setting (https://www.cog-genomics.org/plink/2.0/data#sort_vars ) to determine their output order. In particular, if the end of one .pvar and the beginning of...