Add namespace to getopt functions

[luispedro]

This enables static linking. Otherwise, these functions conflict with the standard getopt functions.

[lh3]

If your system has getopt, then you should use the system getopt for static linking. I have made main.c optionally use system getopt by defining HAVE_GETOPT. For static linking, use the following:

gcc -g -Wall -O2 -Wc++-compat -DHAVE_GETOPT main.c -o minimap2 -L. -lminimap2 -lm -lz -lpthread -static

[luispedro]

Thanks. This is a better solution to the problem than my patch.

[unode]

@lh3 on CentOS 6.6 and using rel v2.12 running:

make CFLAGS="-O2 -DHAVE_GETOPT -static"
(...)
cc -c -O2 -DHAVE_GETOPT -static -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
cc -c -O2 -DHAVE_GETOPT -static -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_dispatch.c -o ksw2_dispatch.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
cc -O2 -DHAVE_GETOPT -static main.o getopt.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libc.a(getopt.o):(.data+0x0): multiple definition of `optind'
getopt.o:(.data+0x0): first defined here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libc.a(getopt.o):(.data+0x4): multiple definition of `opterr'
getopt.o:(.data+0x4): first defined here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libc.a(getopt.o): In function `getopt':
(.text+0x1560): multiple definition of `getopt'
getopt.o:getopt.c:(.text+0xb0): first defined here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libpthread.a(libpthread.o): In function `sem_open':
(.text+0x77cd): warning: the use of `mktemp' is dangerous, better use `mkstemp'
collect2: ld returned 1 exit status
make[1]: *** [minimap2] Error 1

still failed linking. Having -DHAVE_GETOPT was insufficient.

Running the gcc command listed above worked around the problem but that command explicitly doesn't include getopt.o.

Any chance of also having this fixed in the makefile?

[lh3]

The github HEAD uses a different command-line argument parser, which is functionally equivalent to getopt. It won't have this issue any more.