compile fix; initialize alignment struct

[sjaenick]

$ g++ --version
g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[ 25%] Building CXX object CMakeFiles/salib.dir/src/aln.cpp.o
In file included from /home/sj/strobealign/src/aln.hpp:10,
                 from /home/sj/strobealign/src/aln.cpp:1:
/home/sj/strobealign/src/sam.hpp: In function ‘Alignment {anonymous}::extend_seed(const Aligner&, const Nam&, const References&, const Read&, bool)’:
/home/sj/strobealign/src/sam.hpp:12:8: error: ‘alignment.Alignment::ref_id’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   12 | struct Alignment {
      |        ^~~~~~~~~
/home/sj/strobealign/src/aln.cpp:255:23: note: ‘alignment.Alignment::ref_id’ was declared here
  255 |             Alignment alignment;
      |                       ^~~~~~~~~
In file included from /home/sj/strobealign/src/aln.hpp:10,
                 from /home/sj/strobealign/src/aln.cpp:1:
/home/sj/strobealign/src/sam.hpp:12:8: error: ‘alignment.Alignment::global_ed’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   12 | struct Alignment {
      |        ^~~~~~~~~
/home/sj/strobealign/src/aln.cpp:255:23: note: ‘alignment.Alignment::global_ed’ was declared here
  255 |             Alignment alignment;
      |                       ^~~~~~~~~
In file included from /home/sj/strobealign/src/aln.hpp:10,
                 from /home/sj/strobealign/src/aln.cpp:1:
/home/sj/strobealign/src/sam.hpp:12:8: error: ‘alignment.Alignment::length’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   12 | struct Alignment {
      |        ^~~~~~~~~
/home/sj/strobealign/src/aln.cpp:255:23: note: ‘alignment.Alignment::length’ was declared here
  255 |             Alignment alignment;
      |                       ^~~~~~~~~
In file included from /home/sj/strobealign/src/aln.hpp:10,
                 from /home/sj/strobealign/src/aln.cpp:1:
/home/sj/strobealign/src/sam.hpp:12:8: error: ‘alignment.Alignment::is_revcomp’ may be used uninitialized in this function [-Werror=maybe-uninitialized]
   12 | struct Alignment {
      |        ^~~~~~~~~
/home/sj/strobealign/src/aln.cpp:255:23: note: ‘alignment.Alignment::is_revcomp’ was declared here
  255 |             Alignment alignment;
      |                       ^~~~~~~~~
cc1plus: some warnings being treated as errors
make[2]: *** [CMakeFiles/salib.dir/build.make:167: CMakeFiles/salib.dir/src/aln.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:157: CMakeFiles/salib.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

[marcelm]

Thanks! Very strange that g++ 12, which I’m using, doesn’t show the error. Also interesting to see that the results change very slightly (only for paired-end reads), so it would appear that we were actually using the uninitialized values somehow. I’m not sure how, but I think Sam::add_pair would be the place to look for if we want to know exactly.

Note I’m merging this manually because I needed to change your commit message and I failed to push to your branch (apparently because it’s also named main).