google_api_genomics

# Copyright 2017 Google Inc.
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# NOTE: This class is auto generated by the swagger code generator program.
# https://github.com/swagger-api/swagger-codegen.git
# Do not edit the class manually.

defmodule GoogleApi.Genomics.V1.Model.Read do
  @moduledoc """
  A read alignment describes a linear alignment of a string of DNA to a reference sequence, in addition to metadata about the fragment (the molecule of DNA sequenced) and the read (the bases which were read by the sequencer). A read is equivalent to a line in a SAM file. A read belongs to exactly one read group and exactly one read group set.  ### Reverse-stranded reads  Mapped reads (reads having a non-null `alignment`) can be aligned to either the forward or the reverse strand of their associated reference. Strandedness of a mapped read is encoded by `alignment.position.reverseStrand`.  If we consider the reference to be a forward-stranded coordinate space of `[0, reference.length)` with `0` as the left-most position and `reference.length` as the right-most position, reads are always aligned left to right. That is, `alignment.position.position` always refers to the left-most reference coordinate and `alignment.cigar` describes the alignment of this read to the reference from left to right. All per-base fields such as `alignedSequence` and `alignedQuality` share this same left-to-right orientation; this is true of reads which are aligned to either strand. For reverse-stranded reads, this means that `alignedSequence` is the reverse complement of the bases that were originally reported by the sequencing machine.  ### Generating a reference-aligned sequence string  When interacting with mapped reads, it's often useful to produce a string representing the local alignment of the read to reference. The following pseudocode demonstrates one way of doing this:      out = \"\"     offset = 0     for c in read.alignment.cigar {       switch c.operation {       case \"ALIGNMENT_MATCH\", \"SEQUENCE_MATCH\", \"SEQUENCE_MISMATCH\":         out += read.alignedSequence[offset:offset+c.operationLength]         offset += c.operationLength         break       case \"CLIP_SOFT\", \"INSERT\":         offset += c.operationLength         break       case \"PAD\":         out += repeat(\"*\", c.operationLength)         break       case \"DELETE\":         out += repeat(\"-\", c.operationLength)         break       case \"SKIP\":         out += repeat(\" \", c.operationLength)         break       case \"CLIP_HARD\":         break       }     }     return out  ### Converting to SAM's CIGAR string  The following pseudocode generates a SAM CIGAR string from the `cigar` field. Note that this is a lossy conversion (`cigar.referenceSequence` is lost).      cigarMap = {       \"ALIGNMENT_MATCH\": \"M\",       \"INSERT\": \"I\",       \"DELETE\": \"D\",       \"SKIP\": \"N\",       \"CLIP_SOFT\": \"S\",       \"CLIP_HARD\": \"H\",       \"PAD\": \"P\",       \"SEQUENCE_MATCH\": \"=\",       \"SEQUENCE_MISMATCH\": \"X\",     }     cigarStr = \"\"     for c in read.alignment.cigar {       cigarStr += c.operationLength + cigarMap[c.operation]     }     return cigarStr

  ## Attributes

  - info (%{optional(String.t) => [ErrorUnknown]}): A map of additional read alignment information. This must be of the form map<string, string[]> (string key mapping to a list of string values). Defaults to: `null`.
  - alignedQuality ([integer()]): The quality of the read sequence contained in this alignment record (equivalent to QUAL in SAM). `alignedSequence` and `alignedQuality` may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence. Defaults to: `null`.
  - alignedSequence (String.t): The bases of the read sequence contained in this alignment record, **without CIGAR operations applied** (equivalent to SEQ in SAM). `alignedSequence` and `alignedQuality` may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence. Defaults to: `null`.
  - alignment (LinearAlignment): The linear alignment for this alignment record. This field is null for unmapped reads. Defaults to: `null`.
  - duplicateFragment (boolean()): The fragment is a PCR or optical duplicate (SAM flag 0x400). Defaults to: `null`.
  - failedVendorQualityChecks (boolean()): Whether this read did not pass filters, such as platform or vendor quality controls (SAM flag 0x200). Defaults to: `null`.
  - fragmentLength (integer()): The observed length of the fragment, equivalent to TLEN in SAM. Defaults to: `null`.
  - fragmentName (String.t): The fragment name. Equivalent to QNAME (query template name) in SAM. Defaults to: `null`.
  - id (String.t): The server-generated read ID, unique across all reads. This is different from the `fragmentName`. Defaults to: `null`.
  - nextMatePosition (Position): The mapping of the primary alignment of the `(readNumber+1)%numberReads` read in the fragment. It replaces mate position and mate strand in SAM. Defaults to: `null`.
  - numberReads (integer()): The number of reads in the fragment (extension to SAM flag 0x1). Defaults to: `null`.
  - properPlacement (boolean()): The orientation and the distance between reads from the fragment are consistent with the sequencing protocol (SAM flag 0x2). Defaults to: `null`.
  - readGroupId (String.t): The ID of the read group this read belongs to. A read belongs to exactly one read group. This is a server-generated ID which is distinct from SAM's RG tag (for that value, see ReadGroup.name). Defaults to: `null`.
  - readGroupSetId (String.t): The ID of the read group set this read belongs to. A read belongs to exactly one read group set. Defaults to: `null`.
  - readNumber (integer()): The read number in sequencing. 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80. Defaults to: `null`.
  - secondaryAlignment (boolean()): Whether this alignment is secondary. Equivalent to SAM flag 0x100. A secondary alignment represents an alternative to the primary alignment for this read. Aligners may return secondary alignments if a read can map ambiguously to multiple coordinates in the genome. By convention, each read has one and only one alignment where both `secondaryAlignment` and `supplementaryAlignment` are false. Defaults to: `null`.
  - supplementaryAlignment (boolean()): Whether this alignment is supplementary. Equivalent to SAM flag 0x800. Supplementary alignments are used in the representation of a chimeric alignment. In a chimeric alignment, a read is split into multiple linear alignments that map to different reference contigs. The first linear alignment in the read will be designated as the representative alignment; the remaining linear alignments will be designated as supplementary alignments. These alignments may have different mapping quality scores. In each linear alignment in a chimeric alignment, the read will be hard clipped. The `alignedSequence` and `alignedQuality` fields in the alignment record will only represent the bases for its respective linear alignment. Defaults to: `null`.
  """

  use GoogleApi.Gax.ModelBase

  @type t :: %__MODULE__{
          :info => map(),
          :alignedQuality => list(any()),
          :alignedSequence => any(),
          :alignment => GoogleApi.Genomics.V1.Model.LinearAlignment.t(),
          :duplicateFragment => any(),
          :failedVendorQualityChecks => any(),
          :fragmentLength => any(),
          :fragmentName => any(),
          :id => any(),
          :nextMatePosition => GoogleApi.Genomics.V1.Model.Position.t(),
          :numberReads => any(),
          :properPlacement => any(),
          :readGroupId => any(),
          :readGroupSetId => any(),
          :readNumber => any(),
          :secondaryAlignment => any(),
          :supplementaryAlignment => any()
        }

  field(:info, type: :map)
  field(:alignedQuality, type: :list)
  field(:alignedSequence)
  field(:alignment, as: GoogleApi.Genomics.V1.Model.LinearAlignment)
  field(:duplicateFragment)
  field(:failedVendorQualityChecks)
  field(:fragmentLength)
  field(:fragmentName)
  field(:id)
  field(:nextMatePosition, as: GoogleApi.Genomics.V1.Model.Position)
  field(:numberReads)
  field(:properPlacement)
  field(:readGroupId)
  field(:readGroupSetId)
  field(:readNumber)
  field(:secondaryAlignment)
  field(:supplementaryAlignment)
end

defimpl Poison.Decoder, for: GoogleApi.Genomics.V1.Model.Read do
  def decode(value, options) do
    GoogleApi.Genomics.V1.Model.Read.decode(value, options)
  end
end

defimpl Poison.Encoder, for: GoogleApi.Genomics.V1.Model.Read do
  def encode(value, options) do
    GoogleApi.Gax.ModelBase.encode(value, options)
  end
end