tests/Makefile, Makefile: make mark_failed_tests_as_todo

When the global test suite is passing, individual failed tests (counted in SHOULD_*_EXPECTED_FAILS)
can be marked as 'TODO' to make continuous integration happy

Makefile

@@ -27,6 +27,7 @@ test:
 	@echo "*** All tests passed. Congratulations !"
 	@echo
 	$(MAKE) -C algo/tests snapshot_success
+	$(MAKE) -C algo/tests mark_failed_tests_as_todo
 
 snapshot_diff:
 	$(MAKE) -C algo/tests snapshot_diff

algo/tests/Makefile

@@ -82,6 +82,11 @@ shouldvdj_with_rc_merged:
 	cat $(SHOULD_VDJ) > should-vdj-tests/should-vdj.merged.fa
 	$(SHOULD_VDJ_TO_TAP) -r should-vdj-tests/should-vdj.merged.fa
 
+# When the global test suite is passing, individual failed tests (counted in SHOULD_*_EXPECTED_FAILS)
+# can be marked as 'TODO' to make continuous integration happy
+mark_failed_tests_as_todo:
+	sed -i "s/^\(not ok [0-9]*\) /\1 # TODO ##/" */*.tap
+
 curatedvdj_archive: curated-vdj.zip
 curated-vdj.zip: $(SHOULD_VDJ_ARCHIVE)
 	$(eval tmpdir := $(shell mktemp -d))