vg
tools for working with variation graphs
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Public Attributes | |
string | sequence = 1 |
The sequence that has been aligned. | |
Path | path = 2 |
The Path that the sequence follows in the graph it has been aligned to, containing the Edit s that modify the graph to produce the sequence. | |
string | name = 3 |
The name of the sequence that has been aligned. Similar to read name in BAM. | |
bytes | quality = 4 |
The quality scores for the sequence, as values on a 0-255 scale. | |
int32 | mapping_quality = 5 |
The mapping quality score for the alignment, in Phreds. | |
int32 | score = 6 |
The score for the alignment, in points. | |
int32 | query_position = 7 |
The offset in the query at which this Alignment occurs. | |
reserved | |
Old field 8 has been removed. | |
string | sample_name = 9 |
The name of the sample that produced the aligned read. | |
string | read_group = 10 |
The name of the read group to which the aligned read belongs. | |
Alignment | fragment_prev = 11 |
The previous Alignment in the fragment. Contains just enough information to locate the full Alignment; e.g. contains an Alignment with only a name, or only a graph mapping position. | |
Alignment | fragment_next = 12 |
Similarly, the next Alignment in the fragment. | |
bool | is_secondary = 15 |
Flag marking the Alignment as secondary. All but one maximal-scoring alignment of a given read in a GAM file must be secondary. | |
double | identity = 16 |
Portion of aligned bases that are perfect matches, or 0 if no bases are aligned. | |
repeated< Path > | fragment = 17 |
An estimate of the length of the fragment, if this Alignment is paired. | |
repeated< Locus > | locus = 18 |
The loci that this alignment supports. TODO: get rid of this, we have annotations in our data model again. | |
repeated< Position > | refpos = 19 |
Position of the alignment in reference paths embedded in graph. Each position has a path name, and the Alignment's minimum position along the path as an offset. | |
bool | read_paired = 20 |
SAMTools-style flags. | |
bool | read_mapped = 21 |
bool | mate_unmapped = 22 |
bool | read_on_reverse_strand = 23 |
bool | mate_on_reverse_strand = 24 |
bool | soft_clipped = 25 |
bool | discordant_insert_size = 26 |
double | uniqueness = 27 |
The fraction of bases in the alignment that are covered by MEMs with <=1 total hits in the graph. | |
double | correct = 28 |
Correctness metric 1 = perfectly aligned to truth, 0 = not overlapping true alignment. | |
repeated< int32 > | secondary_score = 29 |
The ordered list of scores of secondary mappings. | |
double | fragment_score = 30 |
Score under the given fragment model, assume higher is better. | |
bool | mate_mapped_to_disjoint_subgraph = 31 |
string | fragment_length_distribution = 32 |
The fragment length distribution under which a paired-end alignment was aligned. | |
reserved | to |
Haplotype-scoring-related fields migrated to the annotation system. | |
double | time_used = 35 |
The time this alignment took. | |
Position | to_correct = 36 |
A path/offset/orientation pair specifying the distance to the correct alignment. | |
bool | correctly_mapped = 37 |
This can be set to true to annotate the Alignment as having been mapped correctly. | |
google protobuf Struct | annotation = 100 |
Annotations carried along with the Alignment. | |
Alignments link query strings, such as other genomes or reads, to Paths.
google protobuf Struct vg::Alignment::annotation = 100 |
Annotations carried along with the Alignment.
double vg::Alignment::correct = 28 |
Correctness metric 1 = perfectly aligned to truth, 0 = not overlapping true alignment.
bool vg::Alignment::correctly_mapped = 37 |
This can be set to true to annotate the Alignment as having been mapped correctly.
bool vg::Alignment::discordant_insert_size = 26 |
repeated<Path> vg::Alignment::fragment = 17 |
An estimate of the length of the fragment, if this Alignment is paired.
string vg::Alignment::fragment_length_distribution = 32 |
The fragment length distribution under which a paired-end alignment was aligned.
Alignment vg::Alignment::fragment_prev = 11 |
double vg::Alignment::fragment_score = 30 |
Score under the given fragment model, assume higher is better.
double vg::Alignment::identity = 16 |
Portion of aligned bases that are perfect matches, or 0 if no bases are aligned.
bool vg::Alignment::is_secondary = 15 |
Flag marking the Alignment as secondary. All but one maximal-scoring alignment of a given read in a GAM file must be secondary.
repeated<Locus> vg::Alignment::locus = 18 |
The loci that this alignment supports. TODO: get rid of this, we have annotations in our data model again.
int32 vg::Alignment::mapping_quality = 5 |
The mapping quality score for the alignment, in Phreds.
bool vg::Alignment::mate_mapped_to_disjoint_subgraph = 31 |
bool vg::Alignment::mate_on_reverse_strand = 24 |
bool vg::Alignment::mate_unmapped = 22 |
string vg::Alignment::name = 3 |
The name of the sequence that has been aligned. Similar to read name in BAM.
Path vg::Alignment::path = 2 |
bytes vg::Alignment::quality = 4 |
The quality scores for the sequence, as values on a 0-255 scale.
int32 vg::Alignment::query_position = 7 |
The offset in the query at which this Alignment occurs.
string vg::Alignment::read_group = 10 |
The name of the read group to which the aligned read belongs.
bool vg::Alignment::read_mapped = 21 |
bool vg::Alignment::read_on_reverse_strand = 23 |
bool vg::Alignment::read_paired = 20 |
SAMTools-style flags.
repeated<Position> vg::Alignment::refpos = 19 |
vg::Alignment::reserved |
Old field 8 has been removed.
string vg::Alignment::sample_name = 9 |
The name of the sample that produced the aligned read.
int32 vg::Alignment::score = 6 |
The score for the alignment, in points.
repeated<int32> vg::Alignment::secondary_score = 29 |
The ordered list of scores of secondary mappings.
string vg::Alignment::sequence = 1 |
The sequence that has been aligned.
bool vg::Alignment::soft_clipped = 25 |
double vg::Alignment::time_used = 35 |
The time this alignment took.
reserved vg::Alignment::to |
Haplotype-scoring-related fields migrated to the annotation system.
Position vg::Alignment::to_correct = 36 |
A path/offset/orientation pair specifying the distance to the correct alignment.
double vg::Alignment::uniqueness = 27 |
The fraction of bases in the alignment that are covered by MEMs with <=1 total hits in the graph.