Fix function prototypes for knetfile and bgzf

[mp15]

Fix function prototypes for knetfile and bgzf to match system read and write.

[pd3]

These changes break compiling on linux. Can you please fix? I undid the merge for now.

[lh3]

Also, we should not use off64_t and lseek64(). They are non-existing on 32-bit Linux, I think (haven't tried). We should use macro to let the system handle off_t and off64_t.

See also: http://www.suse.de/~aj/linux_lfs.html

[mp15]

Thanks Petr, I've fixed it and committed to the misc_improve branch again.

Heng you're right, the reason why the same code worked in samtools but not htslib is that samtools has -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE set by the default makefile. From what I have read LFS is available on 32-bit systems, and is kernel and filesystem dependant (kernel 2.4.0+) rather than architecture dependant. I'd attempted to workaround its non-existence for BSD but you're right relying on the macro system is better. You may wish to have those flags set by default in htslib too? After all we do tend to work with large files. The POSIX way to do this would be to add getconf LFS_CFLAGS to the makefile, not sure if this would work on WIN32 though.

Martin

On 5 Sep 2012, at 17:07, Heng Li wrote:

Also, we should not use off64_t and lseek64(). They are non-existing on 32-bit Linux, I think (haven't tried). We should use macro to let the system handle off_t and off64_t.

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These changes breaks compiling on linux. Can you please fix? I undid the merge for now.

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