System tests on Linux

Workflow runs for System tests on Linux

• Grade adapter, overrepresented, N content and duplication as FastQC

  requires action with the application:
  System tests on Linux#152:Pull request#146openedbyMaximilianStammnitz
  MaximilianStammnitz:fix-grading-units

  Nov 2, 2026Action required
  More actions for workflow run 152

• src/fastq_bgzf_file.cpp: fixing macos compiler complaint about type w…

  completed successfully:
  System tests on Linux#151:Commit99197e7pushedbyandrewdavidsmith
  main

  Oct 28, 20261m 36s
  More actions for workflow run 151

• Fixing bug in decompressing some BGZF files and reporting actual buffer sizes in verbose output

  completed successfully:
  System tests on Linux#150:Pull request#143synchronizebyandrewdavidsmith
  fix-bgzf-crash

  Oct 28, 20261m 24s
  More actions for workflow run 150

• Fixing bug in decompressing some BGZF files and reporting actual buffer sizes in verbose output

  completed successfully:
  System tests on Linux#149:Pull request#143openedbyandrewdavidsmith
  fix-bgzf-crash

  Oct 28, 20261m 21s
  More actions for workflow run 149

• src/fastq_file.cpp: apparently fcntl.h is needed on systems besides m…

  completed successfully:
  System tests on Linux#148:Commit2caf316pushedbyandrewdavidsmith
  main

  Oct 28, 20261m 13s
  More actions for workflow run 148

• Adding robustness to IUPAC degenerate nucleotides in reads

  completed successfully:
  System tests on Linux#147:Pull request#142openedbyandrewdavidsmith
  robustness-to-iupac-degen

  Oct 28, 20261m 18s
  More actions for workflow run 147

• System tests on Linux

  completed successfully:
  System tests on Linux#146:Manually runbyandrewdavidsmith
  robustness-to-iupac-degen

  Oct 28, 20261m 11s
  More actions for workflow run 146

• data/test_data/md5sum.txt: adding test hash for original gc content test

  completed successfully:
  System tests on Linux#144:Commit54af0b2pushedbyandrewdavidsmith
  main

  Oct 12, 20261m 12s
  More actions for workflow run 144

• Mode to output GC content using original FastQC smoothing

  completed successfully:
  System tests on Linux#143:Pull request#140openedbyandrewdavidsmith
  gc-content-grade

  Oct 12, 20261m 1s
  More actions for workflow run 143

• src/falco_analyzer.cpp: catching exceptions within threads for easier…

  completed successfully:
  System tests on Linux#142:Commitf464284pushedbyandrewdavidsmith
  main

  Oct 7, 20261m 19s
  More actions for workflow run 142

• Catching exceptions within threads for easier debugging

  completed successfully:
  System tests on Linux#141:Pull request#139openedbyandrewdavidsmith
  exceptions-from-threads

  Oct 7, 20261m 12s
  More actions for workflow run 141

• reads files: changing type for min_chunk_size because of compiler pro…

  completed successfully:
  System tests on Linux#140:Commit046572cpushedbyandrewdavidsmith
  main

  Oct 6, 20261m 38s
  More actions for workflow run 140

• Falco accepts BAM/SAM files without quality scores and stability added for small inputs

  completed successfully:
  System tests on Linux#139:Pull request#138openedbyandrewdavidsmith
  quals-optional

  Oct 6, 20261m 19s
  More actions for workflow run 139

• src/bgzf_reader.hcpp: moving the gzip file header struct into the sou…

  completed successfully:
  System tests on Linux#138:Commitc85e331pushedbyandrewdavidsmith
  main

  Oct 1, 20261m 16s
  More actions for workflow run 138

• Fixing potentially dangerous memcpy and cleaning up includes and clang-tidy checks

  completed successfully:
  System tests on Linux#137:Pull request#137synchronizebyandrewdavidsmith
  fix-includes2

  Oct 1, 20262m 52s
  More actions for workflow run 137

• Fixing potentially dangerous memcpy and cleaning up includes and clang-tidy checks

  completed successfully:
  System tests on Linux#136:Pull request#137openedbyandrewdavidsmith
  fix-includes2

  Oct 1, 20262m 33s
  More actions for workflow run 136

• Fixing potentially dangerous memcpy and cleaning up includes and clang-tidy checks

  completed successfully:
  System tests on Linux#135:Pull request#136openedbyandrewdavidsmith
  fixed-includes

  Oct 1, 20261m 26s
  More actions for workflow run 135

• src/falco.cpp: formatting

  completed successfully:
  System tests on Linux#134:Commite436027pushedbyandrewdavidsmith
  main

  Sep 30, 20261m 11s
  More actions for workflow run 134

• Fixing misleading user interface message related to memory buffer size

  completed successfully:
  System tests on Linux#133:Pull request#135synchronizebyandrewdavidsmith
  cleanup

  Sep 30, 202656s
  More actions for workflow run 133

• Fixing misleading user interface message related to memory buffer size

  completed successfully:
  System tests on Linux#132:Pull request#135synchronizebyandrewdavidsmith
  cleanup

  Sep 30, 20261m 16s
  More actions for workflow run 132

• Fixing misleading user interface message related to memory buffer size

  completed successfully:
  System tests on Linux#131:Pull request#135openedbyandrewdavidsmith
  cleanup

  Sep 30, 20261m 23s
  More actions for workflow run 131

• data/test_data/md5sum.txt: updating hashes for versions

  completed successfully:
  System tests on Linux#130:Commitfa907d9pushedbyandrewdavidsmith
  main

  Sep 27, 20261m 10s
  More actions for workflow run 130

• Version bump to v2.0.3

  completed successfully:
  System tests on Linux#129:Pull request#131openedbyandrewdavidsmith
  version-bump-to-203

  Sep 27, 20261m 14s
  More actions for workflow run 129

• src/task_queue.hpp: adding forgotten lock around assignment to stop v…

  completed successfully:
  System tests on Linux#128:Commiteda9f1dpushedbyandrewdavidsmith
  main

  Sep 23, 20261m 11s
  More actions for workflow run 128

• Bug fix in the task queue

  completed successfully:
  System tests on Linux#127:Pull request#130openedbyandrewdavidsmith
  race-fix

  Sep 23, 20261m 52s
  More actions for workflow run 127