search

pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
773 stars 274 forks source link

htslib: Fix mmap configure check for current compilers #1250

Closed fweimer-rh closed 8 months ago

fweimer-rh commented 9 months ago

It is necessary to define _DEFAULT_SOURCE along with _XOPEN_SOURCE, otherwise the configure check for mmap fails with compilers which do not support implicit function declarations because the check relies on the presence of the getpagesize function.

Downstream version of samtools/htslib#1711.

jmarshall commented 8 months ago

Thanks for caring enough to provide a PR for pysam. However this is an HTSlib problem that I anticipate may be resolved in a different way, so we'll close this here and revisit when HTSlib has responded to the problem.