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4dn-dcic / pairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
MIT License
83 stars 13 forks source link

Isoc99 #77

Closed SooLee closed 5 months ago

SooLee commented 5 months ago

Fixing the following error due to recent C standard change.

error: call to undeclared function 'pairs_merger'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
error: call to undeclared function 'stream_1d'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]

This change addresses https://github.com/4dn-dcic/pairix/issues/74

SooLee commented 5 months ago

Please merge and release 0.3.8

robomics commented 3 months ago

Hi! Another issue related to this is the implicit conversion from pointer to integer (-Wint-conversion) which is now treated as an error by clang due to changes in C99 (see here).

This is causing build failures on bioconda's macOS CI - link. One quick workaround would be to update the Makefile to add -Wno-int-conversion, however after looking at the implementation of ti_iter_first() I don't think is a good idea. The function appears to be returning the address of a local variable (which used to be implicitly cast to integer). Can you please confirm that this is this the intended behavior of ti_iter_first()?