Lines Matching full:alignment

97 alignment to the reference genome overlap the range. A query which
157       { # A read alignment describes a linear alignment of a string of DNA to a
169           # Mapped reads (reads having a non-null `alignment`) can be aligned to either
171           # of a mapped read is encoded by `alignment.position.reverseStrand`.
176           # to right. That is, `alignment.position.position` always refers to the
177           # left-most reference coordinate and `alignment.cigar` describes the alignment
188           # representing the local alignment of the read to reference. The following
193           #     for c in read.alignment.cigar {
235           #     for c in read.alignment.cigar {
239         "info": { # A map of additional read alignment information. This must be of the form
248         "alignedQuality": [ # The quality of the read sequence contained in this alignment record
251             # sequence and quality. This will occur if the alignment is part of a
252             # chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
268 …"supplementaryAlignment": True or False, # Whether this alignment is supplementary. Equivalent to …
270             # alignment. In a chimeric alignment, a read is split into multiple
272             # linear alignment in the read will be designated as the representative
273             # alignment; the remaining linear alignments will be designated as
275             # quality scores. In each linear alignment in a chimeric alignment, the read
277             # `alignedQuality` fields in the alignment record will only
278             # represent the bases for its respective linear alignment.
281 …"secondaryAlignment": True or False, # Whether this alignment is secondary. Equivalent to SAM flag…
282             # A secondary alignment represents an alternative to the primary alignment
285             # has one and only one alignment where both `secondaryAlignment`
287 …"alignedSequence": "A String", # The bases of the read sequence contained in this alignment record,
291             # alignment is part of a chimeric alignment, or if the read was trimmed. When
296 …"alignment": { # A linear alignment can be represented by one CIGAR string. Describes the # The li…
298             # mapped position and local alignment of the read to the reference.
299 …traction for referring to a genomic position, in relation to some # The position of this alignment.
308           "cigar": [ # Represents the local alignment of this sequence (alignment matches, indels,
319           "mappingQuality": 42, # The mapping quality of this alignment. Represents how likely
325 … referring to a genomic position, in relation to some # The mapping of the primary alignment of the