As noted in #428, get_bundle.start was never updated. As such get_bundles.check_output only returned do_output=True at the end of a contig which is not the intended behaviour. This PR fixes this.
Note that this also changes the output order for some test files. For each of the test files modified herein, I have manually checked (diff <(sort new_test_output) <(sort old_test_output)) to make sure the only difference is the order of the output.
As noted in #428,
get_bundle.startwas never updated. As suchget_bundles.check_outputonly returneddo_output=Trueat the end of a contig which is not the intended behaviour. This PR fixes this.Note that this also changes the output order for some test files. For each of the test files modified herein, I have manually checked (
diff <(sort new_test_output) <(sort old_test_output)) to make sure the only difference is the order of the output.