Fixes clang++9 error in cram_io.h

[pjotrp]

Even though it is sitting in an extern "C" block the clang++ compiler won't accept this void * assignment.

[pjotrp]

The full error was:

[9/104] Compiling C++ object 'freebayes@exe/src_DataLikelihood.cpp.o'.
FAILED: freebayes@exe/src_DataLikelihood.cpp.o
clang++ -Ifreebayes@exe -I. -I.. -I../src -I../bamtools/src/api -I../bamtools/src -I../ttmath -I../contrib -I../contrib/SeqLib -I../contrib/htslib_config -I../contrib/htslib/cram -I../contrib/htslib/htslib -I../contrib/htslib -I../vcflib/src -I../vcflib/tabixpp -I../vcflib/smithwaterman -I../vcflib/multichoose -I../vcflib/filevercmp -I/gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11/include -Xclang -fcolor-diagnostics -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -pthread -fpermissive -w -MD -MQ 'freebayes@exe/src_DataLikelihood.cpp.o' -MF 'freebayes@exe/src_DataLikelihood.cpp.o.d' -o 'freebayes@exe/src_DataLikelihood.cpp.o' -c ../src/DataLikelihood.cpp
In file included from ../src/DataLikelihood.cpp:1:
In file included from ../src/DataLikelihood.h:20:
In file included from ../src/AlleleParser.h:30:
In file included from ../src/LeftAlign.h:99:
In file included from ../contrib/SeqLib/SeqLib/BamReader.h:6:
In file included from ../contrib/SeqLib/SeqLib/BamWalker.h:15:
In file included from ../contrib/htslib/cram/cram.h:48:
../contrib/htslib/cram/cram_io.h:513:20: error: cannot initialize a variable of type 'unsigned char *' with an rvalue of type 'void *'
    unsigned char *tmp = realloc(b->data, len);
                   ^     ~~~~~~~~~~~~~~~~~~~~~
1 error generated.

[jmarshall]

That is indeed the only error from compiling the cram/*.h headers with a C++ compiler so it's probably worth applying this, but the real problem is that freebayes shouldn't be including these private headers. Freebayes should apply walaj/SeqLib#53 to its bundled SeqLib.

[pjotrp]

Thanks. I'll apply the patch to the bundled SeqLib files. I'll remove the implicit cram includes.

[pjotrp]

freebayes now compiles a stock htslib - no more bundled source. Above error may act like a canary in the coal mine ;)

[daviesrob]

Thanks, closing as it appears to be no longer be a problem.

Please raise an issue if you find you still need something like this.

[niemasd]

I think I'm getting this issue on the following line of code when trying to compile htslib with clang++ in a Mac OS X environment:

https://github.com/samtools/htslib/blob/develop/cram/cram_io.h#L217

Here's the error:

https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=42286&view=logs&j=1b052f1d-4456-52f0-9d43-71c4c5bd734d&t=edc48dcd-1fc2-5e3b-7036-7be9cea00123&l=401

EDIT: Quick follow-up, the same fix seemed to have worked:

https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=42290&view=logs&j=1b052f1d-4456-52f0-9d43-71c4c5bd734d&t=edc48dcd-1fc2-5e3b-7036-7be9cea00123&l=286

Specifically, I just did the following before running make:

sed -i.bak 's/unsigned char \*tmp = realloc(b->data, len);/unsigned char \*tmp = (unsigned char \*)realloc(b->data, len);/g' htslib/cram/cram_io.h

which just replaces this:

unsigned char *tmp = realloc(b->data, len);

with this:

unsigned char *tmp = (unsigned char *)realloc(b->data, len);

[jkbonfield]

The public header files should be capable of being included by C++ files, but the actual htslib library (both C and non-public header files) are in C, not C++. We don't make our C code swallowable by C++. That includes the internal cram/cram_io.h file.

Is there a reason you can't build htslib using its own supplied build system?

[jmarshall]

This is bioconda/bioconda-recipes#43322, so the best answer is that @niemasd's recipe should compile against bioconda's packaged htslib instead of building htslib at all.

[daviesrob]

I've made niemasd/ViralConsensus#9, which removes the use of CRAM internals from ViralConsensus.

[niemasd]

Ah, thank you so much, @daviesrob! I couldn't figure out how to use the local reference properly, and this was what I found when I dug through the source code of other tools that use htslib. I appreciate it!

I wonder if it makes sense to have a "How to properly include htslib in your code" guide? I tried looking through the htslib documentation, and I couldn't find anything. Even now that I know the solution, when I Google "hts_set_opt" "cram", I don't find any results that would have suggested this solution, whereas "Load a SAM/BAM/CRAM file and iterate over it" is a very common use-case