[Debian-med-packaging] Bug#907489: Trying sambamba pre-release but meson build needs adapting

[Andreas Tille]

Hi Matthias,

to build sambamba you once added a patch that creates a meson.build
file.  I have no experience with meson at all.  I tried to adapt
meson.build to the move of main.d and the additional source files[1].  I
admit the manual work for cases when upstream adds new source files is
not really friendly - but anyway that's not the current problem.

When trying to build I get:

...
[1/80] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_main.d.o' -c ../sambamba/main.d
FAILED: sambamba at exe/sambamba_main.d.o 
ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_main.d.o' -c ../sambamba/main.d
../sambamba/markdup2.d(46): Error: module `reader` is in file 'bio2/bam/reader.d' which cannot be read
import path[0] = sambamba at exe
import path[1] = .
import path[2] = ..
import path[3] = /usr/include/d
import path[4] = /usr/lib/ldc/x86_64-linux-gnu/include/d/ldc
import path[5] = /usr/lib/ldc/x86_64-linux-gnu/include/d
import path[6] = /usr/include/d
[2/80] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_flagstat.d.o' -c ../sambamba/flagstat.d
[3/80] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_fixbins.d.o' -c ../sambamba/fixbins.d
[4/80] ldc2 -Isambamba at exe -I. -I.. -I/usr/include/d -enable-color -O -g -release -wi   -of 'sambamba at exe/sambamba_depth.d.o' -c ../sambamba/depth.d
ninja: build stopped: subcommand failed.
dh_auto_build: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:9: build] Error 1
...

Unfortunately I have no idea why reader.d is seeked in bio2/bam/reader.d
and how to fix this.

Kind regards

      Andreas.

[1] https://salsa.debian.org/med-team/sambamba/commit/e2e5659edfdd7c08a70f0699f3196a8022c93e48

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