apps/ngs_roi/bam2roi.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 typo fix, interst->interest

util/cmake/SeqAnBuildSystem.cmake | 17 9 + 8 - 0 !
1 file changed, 9 insertions(+), 8 deletions(-)

 don't look for a git directory, as the debian packaging confuses
the build system

tests/arg_parse/test_arg_parse_version_check.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fixes test to work with -dseqan_disable_version_check=yes

apps/razers/CMakeLists.txt | 10 10 + 0 - 0 !
apps/razers3/CMakeLists.txt | 15 15 + 0 - 0 !
apps/searchjoin/CMakeLists.txt | 5 5 + 0 - 0 !
apps/yara/CMakeLists.txt | 38 38 + 0 - 0 !
4 files changed, 68 insertions(+)

 skip some architectures + seqan app combinations
Could be a bug in gcc or seqan, but the memory requirements on mips{,el} to
compile three of the apps balloons beyond 14GiB, so skip them

If you update this patch (add/remove an architecture/app combo),
then update debian/README.Debian

apps/ngs_roi/README | 5 3 + 2 - 0 !
1 file changed, 3 insertions(+), 2 deletions(-)

 update paths to their debian equivalents

apps/fiona/CMakeLists.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 install the illumina version of fiona as well

include/seqan/arg_parse/arg_parse_ctd_support.h | 2 1 + 1 - 0 !
tests/arg_parse/test_app.ctd | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 [patch] [internal] fix ctd output: add ctdversion tag in header.

include/seqan/arg_parse/tool_doc.h | 25 21 + 4 - 0 !
1 file changed, 21 insertions(+), 4 deletions(-)

 [patch] [internal] fixes man page output: escape special characters
 '.' or ''' at the beginning of a line.

include/seqan/basic/basic_stream.h | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 use alignment-safe buffer handling.
 Currently we are using assignment to copy the contents of a variable of
 arbitrary type into a buffer, but this is not portable because the buffer
 address may not be aligned.  Use memcpy() instead, which should be
 comparable performance ut alignment-safe.

include/seqan/parallel/parallel_lock.h | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 fix thread wait for ia64

apps/bs_tools/tests/run_tests.py | 26 13 + 13 - 0 !
apps/dfi/tests/run_tests.py | 26 13 + 13 - 0 !
apps/fiona/tests/run_tests.py | 26 13 + 13 - 0 !
apps/gustaf/tests/run_tests.py | 24 12 + 12 - 0 !
apps/insegt/tests/run_tests.py | 24 12 + 12 - 0 !
apps/mason2/tests/run_tests.py | 26 13 + 13 - 0 !
apps/micro_razers/tests/run_tests.py | 24 12 + 12 - 0 !
apps/ngs_roi/tests/run_tests.py | 24 12 + 12 - 0 !
apps/ngs_roi/tool_shed/ctd2galaxy.py | 12 6 + 6 - 0 !
apps/ngs_roi/tool_shed/ngs_roi/app.py | 8 4 + 4 - 0 !
apps/ngs_roi/tool_shed/ngs_roi/argparse.py | 2 1 + 1 - 0 !
apps/ngs_roi/tool_shed/ngs_roi/io.py | 4 2 + 2 - 0 !
apps/ngs_roi/tool_shed/roi_details.py | 8 4 + 4 - 0 !
apps/ngs_roi/tool_shed/roi_plot_thumbnails.py | 12 6 + 6 - 0 !
apps/ngs_roi/tool_shed/roi_report.py | 4 2 + 2 - 0 !
apps/ngs_roi/tool_shed/roi_table.py | 12 6 + 6 - 0 !
apps/ngs_roi/tool_shed/rois.py | 2 1 + 1 - 0 !
apps/pair_align/tests/run_tests.py | 24 12 + 12 - 0 !
apps/rabema/tests/run_tests.py | 24 12 + 12 - 0 !
apps/razers/gapped_params/dat2cpp.py | 10 5 + 5 - 0 !
apps/razers/tests/run_tests.py | 28 14 + 14 - 0 !
apps/razers3/tests/run_tests.py | 24 12 + 12 - 0 !
apps/razers3/tests/run_tests_sequential.py | 2 1 + 1 - 0 !
apps/sak/tests/run_tests.py | 24 12 + 12 - 0 !
apps/sam2matrix/tests/run_tests.py | 24 12 + 12 - 0 !
apps/samcat/tests/run_tests.py | 24 12 + 12 - 0 !
apps/searchjoin/tests/run_tests.py | 28 14 + 14 - 0 !
apps/seqan_tcoffee/tests/run_tests.py | 28 14 + 14 - 0 !
apps/seqcons2/tests/run_tests.py | 24 12 + 12 - 0 !
apps/sgip/tests/run_tests.py | 24 12 + 12 - 0 !
apps/snp_store/tests/run_tests.py | 24 12 + 12 - 0 !
apps/splazers/tests/run_tests.py | 24 12 + 12 - 0 !
apps/stellar/tests/run_tests.py | 24 12 + 12 - 0 !
apps/tree_recon/tests/run_tests.py | 24 12 + 12 - 0 !
apps/yara/tests/run_tests.py | 28 14 + 14 - 0 !
manual/source/Infrastructure/Manage/WriteAppTests.rst | 2 1 + 1 - 0 !
util/bin/auto_build.py | 2 1 + 1 - 0 !
util/bin/dddoc.py | 2 1 + 1 - 0 !
util/bin/demo_checker.py | 28 14 + 14 - 0 !
util/bin/dox.py | 2 1 + 1 - 0 !
util/bin/fixgcov.py | 2 1 + 1 - 0 !
util/bin/profile2pdf.py | 40 20 + 20 - 0 !
util/bin/pyclangcheck.py | 2 1 + 1 - 0 !
util/bin/skel.py | 2 1 + 1 - 0 !
util/ctd2galaxy.py | 8 4 + 4 - 0 !
util/py_lib/seqan/app_tests.py | 64 32 + 32 - 0 !
util/py_lib/seqan/auto_build.py | 4 2 + 2 - 0 !
util/py_lib/seqan/fixgcov/__init__.py | 4 2 + 2 - 0 !
util/py_lib/seqan/fixgcov/app.py | 30 15 + 15 - 0 !
util/py_lib/seqan/paths.py | 10 5 + 5 - 0 !
util/py_lib/seqan/pyclangcheck/__init__.py | 4 2 + 2 - 0 !
util/py_lib/seqan/pyclangcheck/app.py | 24 12 + 12 - 0 !
util/py_lib/seqan/pyclangcheck/rules.py | 8 4 + 4 - 0 !
util/py_lib/seqan/pyclangcheck/simple_checks.py | 8 4 + 4 - 0 !
util/py_lib/seqan/pyclangcheck/suppressions.py | 2 1 + 1 - 0 !
util/py_lib/seqan/pyclangcheck/violations.py | 20 10 + 10 - 0 !
util/py_lib/seqan/skel.py | 114 57 + 57 - 0 !
util/skel/app_tests_template/run_tests.py | 2 1 + 1 - 0 !
58 files changed, 530 insertions(+), 530 deletions(-)

 python3 conversion

apps/mason2/CMakeLists.txt | 2 1 + 1 - 0 !
util/bin/demo_checker.py | 6 3 + 3 - 0 !
util/py_lib/seqan/app_tests.py | 4 2 + 2 - 0 !
3 files changed, 6 insertions(+), 6 deletions(-)

 fix some string comparisons made
 for py2. In py3 we read bytes, not str, so
 decode bytes to str before comparison.
 Remove mason2 tests as upstream skip them
 if gcc > 10 (in develop branch)
Last-Updated: 2022-12-21