tiddit is using patched BamTools - do we want to incorporate this patch?

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tiddit is using patched BamTools - do we want to incorporate this patch?

Andreas Tille-5
Hi,

as per the COVID-19 list given by Jun I intend to package tiddit[1].  I
just realised that the code copy of Bamtools upstream is shipping is
patched


$ grep -Ri -A1  SUPPLEMENTARY
src/api/BamAlignment.h:         bool IsSupplementaryAlignment(void) const;
src/api/BamAlignment.h-
--
src/api/BamConstants.h:const int SUPPLEMENTARY           = 0x0800;
src/api/BamConstants.h-
--
src/api/BamAlignment.cpp:bool BamAlignment::IsSupplementaryAlignment(void) const {
src/api/BamAlignment.cpp:    return ( (AlignmentFlag & Constants::SUPPLEMENTARY) != 0 );
src/api/BamAlignment.cpp-}


Given that this is a somehow simple addition that should not break
anything I tend to add this to our bamtools package.  But since I'm not
a user of bamtools and have no idea whether there are any side effects
I'd like to discuss this first.  Please note that I did not tested
whether this really fixes the whole build but at least the patch seems
to take this specific hurdle:


/usr/bin/c++   -I/build/tiddit-2.11.0+dfsg/src -I/usr/include/bamtools  -g -O2 -fdebug-prefix-map=/build/tiddit-2.11.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -              D_FORTIFY_SOURCE=2 -O3 -DNDEBUG   -Wno-deprecated -o CMakeFiles/TIDDIT.dir/src/data_structures/findTranslocationsOnTheFly.cpp.o -c /build/tiddit-2.11.0+dfsg/src/data_structures/findTranslocationsOnTheFly.cpp
/build/tiddit-2.11.0+dfsg/src/data_structures/Translocation.cpp: In member function ‘void Window::insertRead(BamTools::BamAlignment, readStatus)’:
/build/tiddit-2.11.0+dfsg/src/data_structures/Translocation.cpp:70:75: error: ‘class BamTools::BamAlignment’ has no member named ‘IsSupplementaryAlignment’
   70 |  if (alignment_split and alignment.IsPrimaryAlignment() and not alignment.IsSupplementaryAlignment() and alignment.MapQuality >= minimum_mapping_quality) {
      |                                                                           ^~~~~~~~~~~~~~~~~~~~~~~~



Any thoughts?

Kind regards

       Andreas.

[1] https://salsa.debian.org/med-team/tiddit

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