MANIFEST.in
README.rst
setup.cfg
setup.py
bin/gfapy-convert
bin/gfapy-mergelinear
bin/gfapy-validate
gfapy/__init__.py
gfapy/byte_array.py
gfapy/error.py
gfapy/field_array.py
gfapy/gfa.py
gfapy/lastpos.py
gfapy/logger.py
gfapy/numeric_array.py
gfapy/oriented_line.py
gfapy/placeholder.py
gfapy/segment_end.py
gfapy/segment_end_path.py
gfapy/sequence.py
gfapy/symbol_invert.py
gfapy.egg-info/PKG-INFO
gfapy.egg-info/SOURCES.txt
gfapy.egg-info/dependency_links.txt
gfapy.egg-info/not-zip-safe
gfapy.egg-info/top_level.txt
gfapy/alignment/__init__.py
gfapy/alignment/alignment.py
gfapy/alignment/cigar.py
gfapy/alignment/placeholder.py
gfapy/alignment/trace.py
gfapy/field/__init__.py
gfapy/field/alignment_gfa1.py
gfapy/field/alignment_gfa2.py
gfapy/field/alignment_list_gfa1.py
gfapy/field/byte_array.py
gfapy/field/char.py
gfapy/field/comment.py
gfapy/field/custom_record_type.py
gfapy/field/field.py
gfapy/field/float.py
gfapy/field/generic.py
gfapy/field/identifier_gfa2.py
gfapy/field/identifier_list_gfa2.py
gfapy/field/integer.py
gfapy/field/json.py
gfapy/field/numeric_array.py
gfapy/field/optional_identifier_gfa2.py
gfapy/field/optional_integer.py
gfapy/field/orientation.py
gfapy/field/oriented_identifier_gfa2.py
gfapy/field/oriented_identifier_list_gfa1.py
gfapy/field/oriented_identifier_list_gfa2.py
gfapy/field/parser.py
gfapy/field/path_name_gfa1.py
gfapy/field/position_gfa1.py
gfapy/field/position_gfa2.py
gfapy/field/segment_name_gfa1.py
gfapy/field/sequence_gfa1.py
gfapy/field/sequence_gfa2.py
gfapy/field/string.py
gfapy/field/validator.py
gfapy/field/writer.py
gfapy/graph_operations/__init__.py
gfapy/graph_operations/artifacts.py
gfapy/graph_operations/copy_number.py
gfapy/graph_operations/graph_operations.py
gfapy/graph_operations/invertible_segments.py
gfapy/graph_operations/linear_paths.py
gfapy/graph_operations/multiplication.py
gfapy/graph_operations/p_bubbles.py
gfapy/graph_operations/redundant_linear_paths.py
gfapy/graph_operations/superfluous_links.py
gfapy/graph_operations/topology.py
gfapy/line/__init__.py
gfapy/line/line.py
gfapy/line/comment/__init__.py
gfapy/line/comment/comment.py
gfapy/line/comment/construction.py
gfapy/line/comment/tags.py
gfapy/line/comment/version_conversion.py
gfapy/line/comment/writer.py
gfapy/line/common/__init__.py
gfapy/line/common/cloning.py
gfapy/line/common/connection.py
gfapy/line/common/construction.py
gfapy/line/common/default_record_definition.py
gfapy/line/common/disconnection.py
gfapy/line/common/dynamic_fields.py
gfapy/line/common/equivalence.py
gfapy/line/common/field_data.py
gfapy/line/common/field_datatype.py
gfapy/line/common/update_references.py
gfapy/line/common/validate.py
gfapy/line/common/version_conversion.py
gfapy/line/common/virtual_to_real.py
gfapy/line/common/writer.py
gfapy/line/custom_record/__init__.py
gfapy/line/custom_record/construction.py
gfapy/line/custom_record/custom_record.py
gfapy/line/edge/__init__.py
gfapy/line/edge/edge.py
gfapy/line/edge/common/__init__.py
gfapy/line/edge/common/alignment_type.py
gfapy/line/edge/common/from_to.py
gfapy/line/edge/containment/__init__.py
gfapy/line/edge/containment/canonical.py
gfapy/line/edge/containment/containment.py
gfapy/line/edge/containment/pos.py
gfapy/line/edge/containment/to_gfa2.py
gfapy/line/edge/gfa1/__init__.py
gfapy/line/edge/gfa1/alignment_type.py
gfapy/line/edge/gfa1/oriented_segments.py
gfapy/line/edge/gfa1/other.py
gfapy/line/edge/gfa1/references.py
gfapy/line/edge/gfa1/to_gfa2.py
gfapy/line/edge/gfa2/__init__.py
gfapy/line/edge/gfa2/alignment_type.py
gfapy/line/edge/gfa2/gfa2.py
gfapy/line/edge/gfa2/other.py
gfapy/line/edge/gfa2/references.py
gfapy/line/edge/gfa2/to_gfa1.py
gfapy/line/edge/link/__init__.py
gfapy/line/edge/link/canonical.py
gfapy/line/edge/link/complement.py
gfapy/line/edge/link/equivalence.py
gfapy/line/edge/link/link.py
gfapy/line/edge/link/references.py
gfapy/line/edge/link/to_gfa2.py
gfapy/line/fragment/__init__.py
gfapy/line/fragment/fragment.py
gfapy/line/fragment/references.py
gfapy/line/gap/__init__.py
gfapy/line/gap/gap.py
gfapy/line/gap/references.py
gfapy/line/group/__init__.py
gfapy/line/group/group.py
gfapy/line/group/gfa2/__init__.py
gfapy/line/group/gfa2/references.py
gfapy/line/group/gfa2/same_id.py
gfapy/line/group/ordered/__init__.py
gfapy/line/group/ordered/captured_path.py
gfapy/line/group/ordered/ordered.py
gfapy/line/group/ordered/references.py
gfapy/line/group/ordered/to_gfa1.py
gfapy/line/group/path/__init__.py
gfapy/line/group/path/captured_path.py
gfapy/line/group/path/path.py
gfapy/line/group/path/references.py
gfapy/line/group/path/to_gfa2.py
gfapy/line/group/path/topology.py
gfapy/line/group/path/validation.py
gfapy/line/group/unordered/__init__.py
gfapy/line/group/unordered/induced_set.py
gfapy/line/group/unordered/references.py
gfapy/line/group/unordered/unordered.py
gfapy/line/header/__init__.py
gfapy/line/header/connection.py
gfapy/line/header/field_data.py
gfapy/line/header/header.py
gfapy/line/header/multiline.py
gfapy/line/header/version_conversion.py
gfapy/line/segment/__init__.py
gfapy/line/segment/coverage.py
gfapy/line/segment/gfa1.py
gfapy/line/segment/gfa1_to_gfa2.py
gfapy/line/segment/gfa2.py
gfapy/line/segment/gfa2_to_gfa1.py
gfapy/line/segment/length_gfa1.py
gfapy/line/segment/references.py
gfapy/line/segment/segment.py
gfapy/line/segment/writer_wo_sequence.py
gfapy/line/unknown/__init__.py
gfapy/line/unknown/unknown.py
gfapy/lines/__init__.py
gfapy/lines/collections.py
gfapy/lines/creators.py
gfapy/lines/destructors.py
gfapy/lines/finders.py
gfapy/lines/headers.py
gfapy/lines/lines.py
manual/gfapy-manual.pdf
tests/__init__.py
tests/extension.py
tests/test_api_alignment.py
tests/test_api_comments.py
tests/test_api_custom_records.py
tests/test_api_extensions.py
tests/test_api_gfa1_lines.py
tests/test_api_gfa2_lines.py
tests/test_api_gfa_basics.py
tests/test_api_header.py
tests/test_api_linear_paths.py
tests/test_api_linear_paths_extended.py
tests/test_api_lines_collections.py
tests/test_api_lines_creators.py
tests/test_api_lines_destructors.py
tests/test_api_lines_finders.py
tests/test_api_multiplication.py
tests/test_api_placeholders.py
tests/test_api_positionals.py
tests/test_api_positions.py
tests/test_api_references_edge_gfa1.py
tests/test_api_references_edge_gfa2.py
tests/test_api_references_f_g_lines.py
tests/test_api_references_groups.py
tests/test_api_references_virtual.py
tests/test_api_rename_lines.py
tests/test_api_tags.py
tests/test_api_version.py
tests/test_api_version_conversion.py
tests/test_gfapy_alignment.py
tests/test_gfapy_byte_array.py
tests/test_gfapy_cigar.py
tests/test_gfapy_line_containment.py
tests/test_gfapy_line_edge.py
tests/test_gfapy_line_header.py
tests/test_gfapy_line_link.py
tests/test_gfapy_line_path.py
tests/test_gfapy_line_segment.py
tests/test_gfapy_line_version.py
tests/test_gfapy_numeric_array.py
tests/test_gfapy_segment_references.py
tests/test_gfapy_sequence.py
tests/test_gfapy_trace.py
tests/test_graphop_artifacts.py
tests/test_graphop_copy_number.py
tests/test_internals_field_parser.py
tests/test_internals_field_validator.py
tests/test_internals_field_writer.py
tests/test_internals_tag_datatype.py
tests/test_unit_alignment.py
tests/test_unit_field_array.py
tests/test_unit_gfa_lines.py
tests/test_unit_header.py
tests/test_unit_line.py
tests/test_unit_line_cloning.py
tests/test_unit_line_connection.py
tests/test_unit_line_dynamic_fields.py
tests/test_unit_line_equivalence.py
tests/test_unit_lines_finders.py
tests/test_unit_multiplication.py
tests/test_unit_numeric_array.py
tests/test_unit_oriented_line.py
tests/test_unit_segment_end.py
tests/test_unit_symbol_invert.py
tests/test_unit_unknown.py
tests/testdata/all_line_types.gfa1.gfa
tests/testdata/all_line_types.gfa2.gfa
tests/testdata/copynum.1.gfa
tests/testdata/copynum.1.gfa2
tests/testdata/copynum.2.gfa
tests/testdata/copynum.2.gfa2
tests/testdata/dead_ends.gfa
tests/testdata/dead_ends.gfa2
tests/testdata/example1.gfa
tests/testdata/example1.gfa2
tests/testdata/example_from_spec.gfa
tests/testdata/example_from_spec.gfa2
tests/testdata/example_from_spec.path14.seq
tests/testdata/example_from_spec2.gfa
tests/testdata/example_from_spec2.gfa2
tests/testdata/gfa2_edges_classification.gfa
tests/testdata/linear_merging.1.gfa
tests/testdata/linear_merging.1.gfa2
tests/testdata/linear_merging.2.gfa
tests/testdata/linear_merging.2.gfa2
tests/testdata/linear_merging.3.gfa
tests/testdata/linear_merging.3.gfa2
tests/testdata/linear_merging.4.gfa
tests/testdata/linear_merging.4.gfa2
tests/testdata/linear_merging.5.gfa
tests/testdata/linear_merging.5.gfa2
tests/testdata/links_distri.l1.gfa
tests/testdata/links_distri.l1.gfa2
tests/testdata/links_distri.l1.m2.gfa
tests/testdata/links_distri.l1.m2.gfa2
tests/testdata/links_distri.l2.gfa
tests/testdata/links_distri.l2.gfa2
tests/testdata/links_distri.l2.m2.gfa
tests/testdata/links_distri.l2.m2.gfa2
tests/testdata/links_distri.l2.m2.no_ld.gfa
tests/testdata/links_distri.l2.m2.no_ld.gfa2
tests/testdata/links_distri.l2.m3.gfa
tests/testdata/links_distri.l2.m3.gfa2
tests/testdata/links_distri.l2.m3.no_ld.gfa
tests/testdata/links_distri.l2.m3.no_ld.gfa2
tests/testdata/links_distri.l3.gfa
tests/testdata/links_distri.l3.gfa2
tests/testdata/links_distri.l3.m2.gfa
tests/testdata/links_distri.l3.m2.gfa2
tests/testdata/links_distri.l3.m2.no_ld.gfa
tests/testdata/links_distri.l3.m2.no_ld.gfa2
tests/testdata/loop.gfa
tests/testdata/loop.gfa2
tests/testdata/sample.gfa
tests/testdata/sample.gfa2
tests/testdata/spec_q1.gfa
tests/testdata/spec_q1.gfa2
tests/testdata/spec_q2.gfa
tests/testdata/spec_q2.gfa2
tests/testdata/spec_q2.path_circular.seq
tests/testdata/spec_q2.path_linear.seq
tests/testdata/spec_q3.gfa
tests/testdata/spec_q3.gfa2
tests/testdata/spec_q4.gfa
tests/testdata/spec_q4.gfa2
tests/testdata/spec_q4.path_more_than_circular.seq
tests/testdata/spec_q5.gfa
tests/testdata/spec_q5.gfa2
tests/testdata/spec_q6.gfa
tests/testdata/spec_q6.gfa2
tests/testdata/spec_q7.gfa
tests/testdata/spec_q7.gfa2
tests/testdata/two_components.gfa
tests/testdata/two_components.gfa2