src/CMakeLists.txt | 2 1 + 1 - 0 !
src/toolkit/bamtools_filter.cpp | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 ignore-thirdparty-and-fix-jsoncpp

src/CMakeLists.txt | 69 68 + 1 - 0 !
1 file changed, 68 insertions(+), 1 deletion(-)

 build additional static lib

src/toolkit/bamtools_filter.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix typo caught by lintian.

src/toolkit/bamtools_filter.cpp | 16 6 + 10 - 0 !
1 file changed, 6 insertions(+), 10 deletions(-)

 fix infinite loop on s390x, arm, ppc64el
 const std::string FilterTool::FilterToolPrivate::GetScriptContents()
 loops indefinitely due to fgets() not setting eof flag if
 the call returns data on those platforms.
 The fgetc/ungetc calls then set/clear eof flag indefinitely.

src/api/internal/bam/BamWriter_p.cpp | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 bamtools crashes/corrupts output data on s390x
 The issue was detected in Ubuntu autopkgtests. The call to
 bamtools revert -in sam_spec_example.bam -out out.bam
 fails due to the buffer overflow detected
 This is due to the write loop in
 src/api/internal/bam/BamWriter_p.cpp
 using single byte instead of sizeof(uint32_t) increment to
 swap bytes in the integer data.
 The output file on s390x is corrupted by the write operation.
 bamtools crash with the hardening flags enabled.