Add meson

[armintoepfer]

• Library support and minimap2 executable
  Update kseq.h from htslib HEAD. Otherwise we cannot link
  minimap2 and htslib at the same time.

[lh3]

What's the linking error?

[armintoepfer]

duplicate symbol _ks_destroy in:
    /usr/local/lib/libhts.a(hts.o)
    subprojects/minimap2/libminimap2.a(bseq.c.o)
duplicate symbol _ks_init in:
    /usr/local/lib/libhts.a(hts.o)
    subprojects/minimap2/libminimap2.a(bseq.c.o)
duplicate symbol _ks_getuntil2 in:
    /usr/local/lib/libhts.a(hts.o)
    subprojects/minimap2/libminimap2.a(bseq.c.o)
ld: 3 duplicate symbols for architecture x86_64

[lh3]

What is the exact gcc/g++/ld command line used for linking?

[armintoepfer]

There was an issue with htslib 1.3.2, but works fine with HEAD. I'll go forward and revert my kseq.h update

[lh3]

Thanks a lot for the clarification. Nonetheless, I am concerned with adding a new build system that I will not maintain. Once I add new files, meson will keep out of sync until someone else fix it. This seems not ideal. In addition, other developers will want to add autoconf, cmake, ninja... which will make things worse.

[SoapZA]

@lh3 Please reconsider this. The whole ecosystem is switching to Meson (and not CMake) from the Autotools, due to it's trivial composability and pluggability. For people that want to reuse minimap2, the current make based solution does not scale, due to necessarily leading to recursive Make solutions. Wayland, the Xorg consortium, systemd, GTK+ have all switched to it from their ancient Autotools-based solutions.

[lh3]

The user base of meson seems much smaller than cmake/autoconf right now. I will leave this issue open and revisit at a later time.

[jmarshall]

FYI the linking error has gone away because HTSlib no longer uses kseq.h's kstream itself, since samtools/htslib@71c03b8.

[armintoepfer]

I'll close this. If you want modern build system support, let me know and I can provide it for HEAD.