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|
# 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 \x01(\x08\x12\x16\n\x0equery_position\x18\x05 \x01(\r\x12\r\n\x05score\x18\x04 \x01(\x02\x12\x1c\n\x14number_of_mismatches\x18\x08 \x01(\r\x12\x18\n\x10number_of_indels\x18\t \x01(\r\x12\x1c\n\x14query_aligned_length\x18\x0b \x01(\r\x12\x1d\n\x15target_aligned_length\x18\x0c \x01(\r\x12\x34\n\x13sequence_variations\x18\r \x03(\x0b\x32\x17.goby.SequenceVariation\x12\x14\n\x0cquery_length\x18\n \x01(\r\x12\x17\n\x0fmapping_quality\x18\x0e \x01(\x05\x12\x12\n\npair_flags\x18\x0f \x01(\r\x12\x38\n\x13pair_alignment_link\x18\x10 \x01(\x0b\x32\x1b.goby.RelatedAlignmentEntry\x12\x16\n\x0e\x66ragment_index\x18\x11 \x01(\r\x12\x43\n\x1espliced_forward_alignment_link\x18\x12 \x01(\x0b\x32\x1b.goby.RelatedAlignmentEntry\x12\x44\n\x1fspliced_backward_alignment_link\x18\x16 \x01(\x0b\x32\x1b.goby.RelatedAlignmentEntry\x12\x15\n\rspliced_flags\x18\x13 \x01(\r\x12\x13\n\x0binsert_size\x18\x14 \x01(\x11\x12\x14\n\x0csample_index\x18\x15 \x01(\r\x12\x1f\n\x17query_index_occurrences\x18\x19 \x01(\r\x12\x11\n\tambiguity\x18\x1b \x01(\r\x12\x16\n\x0e\x62\x61m_attributes\x18\x32 \x03(\t\x12\x1b\n\x13read_quality_scores\x18\x37 \x01(\x0c\x12\x19\n\x11read_origin_index\x18\x1a \x01(\r\x12\x1c\n\x14softClippedBasesLeft\x18\x1e \x01(\t\x12\x1d\n\x15softClippedBasesRight\x18\x1f \x01(\t\x12\x1e\n\x16softClippedQualityLeft\x18 \x01(\x0c\x12\x1f\n\x17softClippedQualityRight\x18! \x01(\x0c\x12\x1e\n\x16placedUnmappedSequence\x18( \x01(\t\x12\x1d\n\x15placedUnmappedQuality\x18) \x01(\x0c\x12\x10\n\x08readName\x18* \x01(\t\"p\n\x15RelatedAlignmentEntry\x12\x14\n\x0ctarget_index\x18\x01 \x01(\r\x12\x10\n\x08position\x18\x02 \x01(\r\x12\x16\n\x0e\x66ragment_index\x18\x03 \x01(\r\x12\x17\n\x0foptimized_index\x18\x32 \x01(\r\"g\n\x11SequenceVariation\x12\x0c\n\x04\x66rom\x18\x02 \x01(\t\x12\n\n\x02to\x18\x01 \x01(\t\x12\x10\n\x08position\x18\x03 \x01(\r\x12\x12\n\nread_index\x18\x05 \x01(\r\x12\x12\n\nto_quality\x18\x04 \x01(\x0c\"\xc4\x05\n\x0f\x41lignmentHeader\x12\"\n\x1asmallest_split_query_index\x18\t \x01(\r\x12!\n\x19largest_split_query_index\x18\x0b \x01(\r\x12\x33\n\x12query_name_mapping\x18\x01 \x01(\x0b\x32\x17.goby.IdentifierMapping\x12\x34\n\x13target_name_mapping\x18\x02 \x01(\x0b\x32\x17.goby.IdentifierMapping\x12\x19\n\x11number_of_queries\x18\x05 \x01(\r\x12\x19\n\x11number_of_targets\x18\x06 \x01(\r\x12\x1f\n\x17number_of_aligned_reads\x18\x07 \x01(\r\x12\x18\n\x0cquery_length\x18\x03 \x03(\rB\x02\x18\x01\x12\x1d\n\x15\x63onstant_query_length\x18\n \x01(\r\x12\x15\n\rtarget_length\x18\x08 \x03(\r\x12\x0e\n\x06sorted\x18\r \x01(\x08\x12\x0f\n\x07indexed\x18\x0e \x01(\x08\x12\'\n\x1fquery_lengths_stored_in_entries\x18\x0f \x01(\x08\x12\x14\n\x0c\x61ligner_name\x18\x11 \x01(\t\x12\x17\n\x0f\x61ligner_version\x18\x12 \x01(\t\x12\x0f\n\x07version\x18\x19 \x01(\t\x12\x17\n\x0fsample_basename\x18\x1e \x03(\t\x12#\n\x1bquery_indices_were_permuted\x18\x1a \x01(\x08\x12\x1f\n\x17query_index_occurrences\x18# \x01(\x08\x12#\n\x1b\x61mbiguity_stored_in_entries\x18$ \x01(\x08\x12\x1f\n\x17\x61ll_read_quality_scores\x18( \x01(\x08\x12)\n\x0bread_origin\x18\x1b \x03(\x0b\x32\x14.goby.ReadOriginInfo\";\n\x11IdentifierMapping\x12&\n\x08mappings\x18\x01 \x03(\x0b\x32\x14.goby.IdentifierInfo\"-\n\x0eIdentifierInfo\x12\x0c\n\x04name\x18\x01 \x02(\t\x12\r\n\x05index\x18\x02 \x02(\r\"\x95\x01\n\x0eReadOriginInfo\x12\x14\n\x0corigin_index\x18\x01 \x02(\r\x12\x11\n\torigin_id\x18\x02 \x02(\t\x12\x0e\n\x06sample\x18\x04 \x01(\t\x12\x10\n\x08platform\x18\x05 \x01(\t\x12\x0f\n\x07library\x18\x08 \x01(\t\x12\x15\n\rplatform_unit\x18\x0c \x01(\t\x12\x10\n\x08run_date\x18\x06 \x01(\t\"X\n\x14\x41lignmentTooManyHits\x12\x19\n\x11\x61ligner_threshold\x18\x02 \x02(\r\x12%\n\x04hits\x18\x01 \x03(\x0b\x32\x17.goby.AmbiguousLocation\"b\n\x11\x41mbiguousLocation\x12\x13\n\x0bquery_index\x18\x01 \x02(\r\x12\x1f\n\x17\x61t_least_number_of_hits\x18\x02 \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)
|
