Leonhard Gruenschloss

icon indicating a website link https://gruenschloss.org icon indicating an email [email protected]

icon company @populationgenomics icon location Sydney, Australia

Results 3 issues of Leonhard Gruenschloss

[batch] Use sops for credentials

7 comment

Context: https://hail.zulipchat.com/#narrow/stream/300487-Hail-Batch-Dev/topic/ci_config.20secrets #assign services

Use gnu99 instead of c99, as strdup is not part of C99

With `c99` only, `strdup` is not defined (see https://stackoverflow.com/questions/26284110/strdup-confused-about-warnings-implicit-declaration-makes-pointer-with for context). Consequently, https://github.com/Illumina/DRAGMAP/blob/ef182bda173d1ca9919b93fae99f068802ed20fc/thirdparty/dragen/src/common/hash_generation/gen_hash_table.c#L158 assigns an invalid pointer value to `dir`, which cannot be read afterwards (e.g. using gcc 9 in...

Always call next() on both tokenizers, to make sure both r1 and r2 files are read to the end

There's an edge case where the `r2Tokenizer`'s buffer hasn't read to the end of the `r2` file yet, but the conditional `r1Tokenizer.next() && r2Tokenizer.next()` gets short-circuited, leading to `r2Tokenizer.next()` not...