# Generated by the protocol buffer compiler. DO NOT EDIT! # source: Alignments.proto import sys _b=sys.version_info[0]<3 and (lambda x:x) or (lambda x:x.encode('latin1')) from google.protobuf import descriptor as _descriptor from google.protobuf import message as _message from google.protobuf import reflection as _reflection from google.protobuf import symbol_database as _symbol_database from google.protobuf import descriptor_pb2 # @@protoc_insertion_point(imports) _sym_db = _symbol_database.Default() DESCRIPTOR = _descriptor.FileDescriptor( name='Alignments.proto', package='goby', syntax='proto2', serialized_pb=_b('\n\x10\x41lignments.proto\x12\x04goby\"F\n\x13\x41lignmentCollection\x12/\n\x11\x61lignment_entries\x18\x01 \x03(\x0b\x32\x14.goby.AlignmentEntry\"\x8b\x08\n\x0e\x41lignmentEntry\x12\x14\n\x0cmultiplicity\x18\x07 \x01(\r\x12\x13\n\x0bquery_index\x18\x01 \x01(\r\x12\x14\n\x0ctarget_index\x18\x02 \x01(\r\x12\x10\n\x08position\x18\x03 \x01(\r\x12\x1f\n\x17matching_reverse_strand\x18\x06 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\x02(\r\x12\x17\n\x0flength_of_match\x18\x03 \x01(\r\"j\n\x0e\x41lignmentIndex\x12#\n\x17target_position_offsets\x18\x01 \x03(\rB\x02\x10\x01\x12\x13\n\x07offsets\x18\x02 \x03(\x04\x42\x02\x10\x01\x12\x1e\n\x12\x61\x62solute_positions\x18\x03 \x03(\x04\x42\x02\x10\x01\x42#\n\x1forg.campagnelab.goby.alignmentsH\x01') ) _ALIGNMENTCOLLECTION = _descriptor.Descriptor( name='AlignmentCollection', full_name='goby.AlignmentCollection', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='alignment_entries', full_name='goby.AlignmentCollection.alignment_entries', index=0, number=1, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=26, serialized_end=96, ) _ALIGNMENTENTRY = _descriptor.Descriptor( name='AlignmentEntry', full_name='goby.AlignmentEntry', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='multiplicity', full_name='goby.AlignmentEntry.multiplicity', index=0, number=7, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_index', full_name='goby.AlignmentEntry.query_index', index=1, number=1, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='target_index', full_name='goby.AlignmentEntry.target_index', index=2, number=2, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='position', full_name='goby.AlignmentEntry.position', index=3, number=3, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='matching_reverse_strand', full_name='goby.AlignmentEntry.matching_reverse_strand', index=4, number=6, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_position', full_name='goby.AlignmentEntry.query_position', index=5, number=5, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='score', full_name='goby.AlignmentEntry.score', index=6, number=4, type=2, cpp_type=6, label=1, has_default_value=False, default_value=float(0), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='number_of_mismatches', full_name='goby.AlignmentEntry.number_of_mismatches', index=7, number=8, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='number_of_indels', full_name='goby.AlignmentEntry.number_of_indels', index=8, number=9, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_aligned_length', full_name='goby.AlignmentEntry.query_aligned_length', index=9, number=11, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='target_aligned_length', full_name='goby.AlignmentEntry.target_aligned_length', index=10, number=12, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='sequence_variations', full_name='goby.AlignmentEntry.sequence_variations', index=11, number=13, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_length', full_name='goby.AlignmentEntry.query_length', index=12, number=10, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='mapping_quality', full_name='goby.AlignmentEntry.mapping_quality', index=13, number=14, type=5, cpp_type=1, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='pair_flags', full_name='goby.AlignmentEntry.pair_flags', index=14, number=15, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='pair_alignment_link', full_name='goby.AlignmentEntry.pair_alignment_link', index=15, number=16, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='fragment_index', full_name='goby.AlignmentEntry.fragment_index', index=16, number=17, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='spliced_forward_alignment_link', full_name='goby.AlignmentEntry.spliced_forward_alignment_link', index=17, number=18, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='spliced_backward_alignment_link', full_name='goby.AlignmentEntry.spliced_backward_alignment_link', index=18, number=22, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='spliced_flags', full_name='goby.AlignmentEntry.spliced_flags', index=19, number=19, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='insert_size', full_name='goby.AlignmentEntry.insert_size', index=20, number=20, type=17, cpp_type=1, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='sample_index', full_name='goby.AlignmentEntry.sample_index', index=21, number=21, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_index_occurrences', full_name='goby.AlignmentEntry.query_index_occurrences', index=22, number=25, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='ambiguity', full_name='goby.AlignmentEntry.ambiguity', index=23, number=27, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='bam_attributes', full_name='goby.AlignmentEntry.bam_attributes', index=24, number=50, type=9, cpp_type=9, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='read_quality_scores', full_name='goby.AlignmentEntry.read_quality_scores', index=25, number=55, type=12, cpp_type=9, label=1, has_default_value=False, default_value=_b(""), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='read_origin_index', full_name='goby.AlignmentEntry.read_origin_index', index=26, number=26, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='softClippedBasesLeft', full_name='goby.AlignmentEntry.softClippedBasesLeft', index=27, number=30, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='softClippedBasesRight', full_name='goby.AlignmentEntry.softClippedBasesRight', index=28, number=31, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='softClippedQualityLeft', full_name='goby.AlignmentEntry.softClippedQualityLeft', index=29, number=32, type=12, cpp_type=9, label=1, has_default_value=False, default_value=_b(""), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='softClippedQualityRight', full_name='goby.AlignmentEntry.softClippedQualityRight', index=30, number=33, type=12, cpp_type=9, label=1, has_default_value=False, default_value=_b(""), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='placedUnmappedSequence', full_name='goby.AlignmentEntry.placedUnmappedSequence', index=31, number=40, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='placedUnmappedQuality', full_name='goby.AlignmentEntry.placedUnmappedQuality', index=32, number=41, type=12, cpp_type=9, label=1, has_default_value=False, default_value=_b(""), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='readName', full_name='goby.AlignmentEntry.readName', index=33, number=42, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=99, serialized_end=1134, ) _RELATEDALIGNMENTENTRY = _descriptor.Descriptor( name='RelatedAlignmentEntry', full_name='goby.RelatedAlignmentEntry', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='target_index', full_name='goby.RelatedAlignmentEntry.target_index', index=0, number=1, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='position', full_name='goby.RelatedAlignmentEntry.position', index=1, number=2, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='fragment_index', full_name='goby.RelatedAlignmentEntry.fragment_index', index=2, number=3, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='optimized_index', full_name='goby.RelatedAlignmentEntry.optimized_index', index=3, number=50, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=1136, serialized_end=1248, ) _SEQUENCEVARIATION = _descriptor.Descriptor( name='SequenceVariation', full_name='goby.SequenceVariation', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='from', full_name='goby.SequenceVariation.from', index=0, number=2, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='to', full_name='goby.SequenceVariation.to', index=1, number=1, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='position', full_name='goby.SequenceVariation.position', index=2, number=3, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='read_index', full_name='goby.SequenceVariation.read_index', index=3, number=5, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='to_quality', full_name='goby.SequenceVariation.to_quality', index=4, number=4, type=12, cpp_type=9, label=1, has_default_value=False, default_value=_b(""), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=1250, serialized_end=1353, ) _ALIGNMENTHEADER = _descriptor.Descriptor( name='AlignmentHeader', full_name='goby.AlignmentHeader', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='smallest_split_query_index', full_name='goby.AlignmentHeader.smallest_split_query_index', index=0, number=9, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='largest_split_query_index', full_name='goby.AlignmentHeader.largest_split_query_index', index=1, number=11, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_name_mapping', full_name='goby.AlignmentHeader.query_name_mapping', index=2, number=1, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='target_name_mapping', full_name='goby.AlignmentHeader.target_name_mapping', index=3, number=2, type=11, cpp_type=10, label=1, has_default_value=False, default_value=None, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='number_of_queries', full_name='goby.AlignmentHeader.number_of_queries', index=4, number=5, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='number_of_targets', full_name='goby.AlignmentHeader.number_of_targets', index=5, number=6, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='number_of_aligned_reads', full_name='goby.AlignmentHeader.number_of_aligned_reads', index=6, number=7, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_length', full_name='goby.AlignmentHeader.query_length', index=7, number=3, type=13, cpp_type=3, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\030\001'))), _descriptor.FieldDescriptor( name='constant_query_length', full_name='goby.AlignmentHeader.constant_query_length', index=8, number=10, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='target_length', full_name='goby.AlignmentHeader.target_length', index=9, number=8, type=13, cpp_type=3, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='sorted', full_name='goby.AlignmentHeader.sorted', index=10, number=13, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='indexed', full_name='goby.AlignmentHeader.indexed', index=11, number=14, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_lengths_stored_in_entries', full_name='goby.AlignmentHeader.query_lengths_stored_in_entries', index=12, number=15, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='aligner_name', full_name='goby.AlignmentHeader.aligner_name', index=13, number=17, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='aligner_version', full_name='goby.AlignmentHeader.aligner_version', index=14, number=18, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='version', full_name='goby.AlignmentHeader.version', index=15, number=25, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='sample_basename', full_name='goby.AlignmentHeader.sample_basename', index=16, number=30, type=9, cpp_type=9, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_indices_were_permuted', full_name='goby.AlignmentHeader.query_indices_were_permuted', index=17, number=26, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='query_index_occurrences', full_name='goby.AlignmentHeader.query_index_occurrences', index=18, number=35, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='ambiguity_stored_in_entries', full_name='goby.AlignmentHeader.ambiguity_stored_in_entries', index=19, number=36, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='all_read_quality_scores', full_name='goby.AlignmentHeader.all_read_quality_scores', index=20, number=40, type=8, cpp_type=7, label=1, has_default_value=False, default_value=False, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='read_origin', full_name='goby.AlignmentHeader.read_origin', index=21, number=27, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=1356, serialized_end=2064, ) _IDENTIFIERMAPPING = _descriptor.Descriptor( name='IdentifierMapping', full_name='goby.IdentifierMapping', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='mappings', full_name='goby.IdentifierMapping.mappings', index=0, number=1, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2066, serialized_end=2125, ) _IDENTIFIERINFO = _descriptor.Descriptor( name='IdentifierInfo', full_name='goby.IdentifierInfo', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='name', full_name='goby.IdentifierInfo.name', index=0, number=1, type=9, cpp_type=9, label=2, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='index', full_name='goby.IdentifierInfo.index', index=1, number=2, type=13, cpp_type=3, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2127, serialized_end=2172, ) _READORIGININFO = _descriptor.Descriptor( name='ReadOriginInfo', full_name='goby.ReadOriginInfo', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='origin_index', full_name='goby.ReadOriginInfo.origin_index', index=0, number=1, type=13, cpp_type=3, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='origin_id', full_name='goby.ReadOriginInfo.origin_id', index=1, number=2, type=9, cpp_type=9, label=2, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='sample', full_name='goby.ReadOriginInfo.sample', index=2, number=4, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='platform', full_name='goby.ReadOriginInfo.platform', index=3, number=5, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='library', full_name='goby.ReadOriginInfo.library', index=4, number=8, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='platform_unit', full_name='goby.ReadOriginInfo.platform_unit', index=5, number=12, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='run_date', full_name='goby.ReadOriginInfo.run_date', index=6, number=6, type=9, cpp_type=9, label=1, has_default_value=False, default_value=_b("").decode('utf-8'), message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2175, serialized_end=2324, ) _ALIGNMENTTOOMANYHITS = _descriptor.Descriptor( name='AlignmentTooManyHits', full_name='goby.AlignmentTooManyHits', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='aligner_threshold', full_name='goby.AlignmentTooManyHits.aligner_threshold', index=0, number=2, type=13, cpp_type=3, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='hits', full_name='goby.AlignmentTooManyHits.hits', index=1, number=1, type=11, cpp_type=10, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2326, serialized_end=2414, ) _AMBIGUOUSLOCATION = _descriptor.Descriptor( name='AmbiguousLocation', full_name='goby.AmbiguousLocation', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='query_index', full_name='goby.AmbiguousLocation.query_index', index=0, number=1, type=13, cpp_type=3, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='at_least_number_of_hits', full_name='goby.AmbiguousLocation.at_least_number_of_hits', index=1, number=2, type=13, cpp_type=3, label=2, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), _descriptor.FieldDescriptor( name='length_of_match', full_name='goby.AmbiguousLocation.length_of_match', index=2, number=3, type=13, cpp_type=3, label=1, has_default_value=False, default_value=0, message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=None), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2416, serialized_end=2514, ) _ALIGNMENTINDEX = _descriptor.Descriptor( name='AlignmentIndex', full_name='goby.AlignmentIndex', filename=None, file=DESCRIPTOR, containing_type=None, fields=[ _descriptor.FieldDescriptor( name='target_position_offsets', full_name='goby.AlignmentIndex.target_position_offsets', index=0, number=1, type=13, cpp_type=3, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001'))), _descriptor.FieldDescriptor( name='offsets', full_name='goby.AlignmentIndex.offsets', index=1, number=2, type=4, cpp_type=4, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001'))), _descriptor.FieldDescriptor( name='absolute_positions', full_name='goby.AlignmentIndex.absolute_positions', index=2, number=3, type=4, cpp_type=4, label=3, has_default_value=False, default_value=[], message_type=None, enum_type=None, containing_type=None, is_extension=False, extension_scope=None, options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001'))), ], extensions=[ ], nested_types=[], enum_types=[ ], options=None, is_extendable=False, syntax='proto2', extension_ranges=[], oneofs=[ ], serialized_start=2516, serialized_end=2622, ) _ALIGNMENTCOLLECTION.fields_by_name['alignment_entries'].message_type = _ALIGNMENTENTRY _ALIGNMENTENTRY.fields_by_name['sequence_variations'].message_type = _SEQUENCEVARIATION _ALIGNMENTENTRY.fields_by_name['pair_alignment_link'].message_type = _RELATEDALIGNMENTENTRY _ALIGNMENTENTRY.fields_by_name['spliced_forward_alignment_link'].message_type = _RELATEDALIGNMENTENTRY _ALIGNMENTENTRY.fields_by_name['spliced_backward_alignment_link'].message_type = _RELATEDALIGNMENTENTRY _ALIGNMENTHEADER.fields_by_name['query_name_mapping'].message_type = _IDENTIFIERMAPPING _ALIGNMENTHEADER.fields_by_name['target_name_mapping'].message_type = _IDENTIFIERMAPPING _ALIGNMENTHEADER.fields_by_name['read_origin'].message_type = _READORIGININFO _IDENTIFIERMAPPING.fields_by_name['mappings'].message_type = _IDENTIFIERINFO _ALIGNMENTTOOMANYHITS.fields_by_name['hits'].message_type = _AMBIGUOUSLOCATION DESCRIPTOR.message_types_by_name['AlignmentCollection'] = _ALIGNMENTCOLLECTION DESCRIPTOR.message_types_by_name['AlignmentEntry'] = _ALIGNMENTENTRY DESCRIPTOR.message_types_by_name['RelatedAlignmentEntry'] = _RELATEDALIGNMENTENTRY DESCRIPTOR.message_types_by_name['SequenceVariation'] = _SEQUENCEVARIATION DESCRIPTOR.message_types_by_name['AlignmentHeader'] = _ALIGNMENTHEADER DESCRIPTOR.message_types_by_name['IdentifierMapping'] = _IDENTIFIERMAPPING DESCRIPTOR.message_types_by_name['IdentifierInfo'] = _IDENTIFIERINFO DESCRIPTOR.message_types_by_name['ReadOriginInfo'] = _READORIGININFO DESCRIPTOR.message_types_by_name['AlignmentTooManyHits'] = _ALIGNMENTTOOMANYHITS DESCRIPTOR.message_types_by_name['AmbiguousLocation'] = _AMBIGUOUSLOCATION DESCRIPTOR.message_types_by_name['AlignmentIndex'] = _ALIGNMENTINDEX _sym_db.RegisterFileDescriptor(DESCRIPTOR) AlignmentCollection = _reflection.GeneratedProtocolMessageType('AlignmentCollection', (_message.Message,), dict( DESCRIPTOR = _ALIGNMENTCOLLECTION, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AlignmentCollection) )) _sym_db.RegisterMessage(AlignmentCollection) AlignmentEntry = _reflection.GeneratedProtocolMessageType('AlignmentEntry', (_message.Message,), dict( DESCRIPTOR = _ALIGNMENTENTRY, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AlignmentEntry) )) _sym_db.RegisterMessage(AlignmentEntry) RelatedAlignmentEntry = _reflection.GeneratedProtocolMessageType('RelatedAlignmentEntry', (_message.Message,), dict( DESCRIPTOR = _RELATEDALIGNMENTENTRY, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.RelatedAlignmentEntry) )) _sym_db.RegisterMessage(RelatedAlignmentEntry) SequenceVariation = _reflection.GeneratedProtocolMessageType('SequenceVariation', (_message.Message,), dict( DESCRIPTOR = _SEQUENCEVARIATION, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.SequenceVariation) )) _sym_db.RegisterMessage(SequenceVariation) AlignmentHeader = _reflection.GeneratedProtocolMessageType('AlignmentHeader', (_message.Message,), dict( DESCRIPTOR = _ALIGNMENTHEADER, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AlignmentHeader) )) _sym_db.RegisterMessage(AlignmentHeader) IdentifierMapping = _reflection.GeneratedProtocolMessageType('IdentifierMapping', (_message.Message,), dict( DESCRIPTOR = _IDENTIFIERMAPPING, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.IdentifierMapping) )) _sym_db.RegisterMessage(IdentifierMapping) IdentifierInfo = _reflection.GeneratedProtocolMessageType('IdentifierInfo', (_message.Message,), dict( DESCRIPTOR = _IDENTIFIERINFO, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.IdentifierInfo) )) _sym_db.RegisterMessage(IdentifierInfo) ReadOriginInfo = _reflection.GeneratedProtocolMessageType('ReadOriginInfo', (_message.Message,), dict( DESCRIPTOR = _READORIGININFO, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.ReadOriginInfo) )) _sym_db.RegisterMessage(ReadOriginInfo) AlignmentTooManyHits = _reflection.GeneratedProtocolMessageType('AlignmentTooManyHits', (_message.Message,), dict( DESCRIPTOR = _ALIGNMENTTOOMANYHITS, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AlignmentTooManyHits) )) _sym_db.RegisterMessage(AlignmentTooManyHits) AmbiguousLocation = _reflection.GeneratedProtocolMessageType('AmbiguousLocation', (_message.Message,), dict( DESCRIPTOR = _AMBIGUOUSLOCATION, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AmbiguousLocation) )) _sym_db.RegisterMessage(AmbiguousLocation) AlignmentIndex = _reflection.GeneratedProtocolMessageType('AlignmentIndex', (_message.Message,), dict( DESCRIPTOR = _ALIGNMENTINDEX, __module__ = 'Alignments_pb2' # @@protoc_insertion_point(class_scope:goby.AlignmentIndex) )) _sym_db.RegisterMessage(AlignmentIndex) DESCRIPTOR.has_options = True DESCRIPTOR._options = _descriptor._ParseOptions(descriptor_pb2.FileOptions(), _b('\n\037org.campagnelab.goby.alignmentsH\001')) _ALIGNMENTHEADER.fields_by_name['query_length'].has_options = True _ALIGNMENTHEADER.fields_by_name['query_length']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\030\001')) _ALIGNMENTINDEX.fields_by_name['target_position_offsets'].has_options = True _ALIGNMENTINDEX.fields_by_name['target_position_offsets']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001')) _ALIGNMENTINDEX.fields_by_name['offsets'].has_options = True _ALIGNMENTINDEX.fields_by_name['offsets']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001')) _ALIGNMENTINDEX.fields_by_name['absolute_positions'].has_options = True _ALIGNMENTINDEX.fields_by_name['absolute_positions']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), _b('\020\001')) # @@protoc_insertion_point(module_scope)