*~ *.dSYM .DS_Store tags *-debug *-s *-l hisat2.xcodeproj/project.xcworkspace hisat2.xcodeproj/xcuserdata hisat2.xcodeproj/xcshareddata *.patch build_automaton build_index clean_alignment determinize gcsa_alignment gcsa_test hisat2-repeat hisat2_test/*.bt2 hisat2_test/*.ht2 hisat2_test/*.sam hisat2_test/paper_example.malignment.automaton hisat2_test/paper_example.malignment.backbone hisat2_test/paper_example.malignment.gcsa hisat2_test/kim_example*.malignment.automaton hisat2_test/kim_example*.malignment.backbone hisat2_test/kim_example*.malignment.gcsa hisat2_test/genome* hisat2_test/2* hisat2_test/snp142* hisat2_test/testset* .idea .vscode .ht2lib-obj* *.a *.so docs/_site docs/*.lock docs/.*-cache *.tar.gz *.ipynb *.pyc cmake*