Help for next version of freebayes needed: libseqlib build error

[Andreas Tille <andreas@an3as.eu>]

Hi,

Version 1.1.x of freebayes needs libseqlib and I commited some
preliminary packaging to Git[1].  My obviously poor attempt to use
Debian packaged libraries instead of code copies endet up in

...
g++ -DHAVE_CONFIG_H -I. -I..  -I../ -I../htslib -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g  -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/build/libseqlib-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_a-SeqPlot.o `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp
In file included from ../SeqLib/UnalignedSequence.h:5:0,
                 from ../SeqLib/BamRecord.h:23,
                 from ../SeqLib/BFC.h:8,
                 from BFC.cpp:33:
/usr/include/bwa/bwa.h:33:3: error: conflicting declaration ‘typedef struct bseq1_t bseq1_t’
 } bseq1_t;
   ^~~~~~~
In file included from ../SeqLib/BFC.h:5:0,
                 from BFC.cpp:33:
/usr/include/fml.h:11:3: note: previous declaration as ‘typedef struct bseq1_t bseq1_t’
 } bseq1_t;
   ^~~~~~~
In file included from ../SeqLib/UnalignedSequence.h:5:0,
                 from ../SeqLib/BamRecord.h:23,
                 from ../SeqLib/BFC.h:8,
                 from BFC.cpp:33:
/usr/include/bwa/bwa.h:42:11: error: conflicting declaration of C function ‘bseq1_t* bseq_read(int, int*, void*, void*)’
  bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);
           ^~~~~~~~~
...


If you want to make this your riddle for the weekend and you
can come up with a solution this would simplify upgrading
freebayes.

Kind regards

       Andreas.


[1] https://anonscm.debian.org/git/debian-med/libseqlib.git

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