| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| 0001-ignore-thirdparty-and-fix-jsoncpp.patch | ignore-thirdparty-and-fix-jsoncpp | Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> | not-needed | 2012-11-07 | ||
| shared_and_static.patch | Build additional static lib | Andreas Tille <tille@debian.org> | no | 2020-05-27 | ||
| typo.patch | fix typo caught by lintian. | Étienne Mollier <emollier@debian.org> | yes | 2023-12-15 | ||
| filter_script.patch | 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. diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp index 16a1b0d..9c2ea44 100644 |
Vladimir Petko <vladimir.petko@canonical.com> | yes | debian upstream | 2024-07-09 | |
| do_not_corrupt_output.patch | 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. |
Vladimir Petko <vladimir.petko@canonical.com> | yes | debian upstream | 2024-07-09 |