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This repository implements GA4GH schemas
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.ga4gh.models;
@SuppressWarnings("all")
/** A linear alignment describes the alignment of a read to a Reference, using a
position and CIGAR array. */
@org.apache.avro.specific.AvroGenerated
public class LinearAlignment extends org.apache.avro.specific.SpecificRecordBase implements org.apache.avro.specific.SpecificRecord {
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"record\",\"name\":\"LinearAlignment\",\"namespace\":\"org.ga4gh.models\",\"doc\":\"A linear alignment describes the alignment of a read to a Reference, using a\\nposition and CIGAR array.\",\"fields\":[{\"name\":\"position\",\"type\":{\"type\":\"record\",\"name\":\"Position\",\"doc\":\"A `Position` is an unoriented base in some `Reference`. A `Position` is\\nrepresented by a `Reference` name, and a base number on that `Reference`\\n(0-based).\",\"fields\":[{\"name\":\"referenceName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The name of the `Reference` on which the `Position` is located.\"},{\"name\":\"position\",\"type\":\"long\",\"doc\":\"The 0-based offset from the start of the forward strand for that `Reference`.\\n Genomic positions are non-negative integers less than `Reference` length.\"},{\"name\":\"strand\",\"type\":{\"type\":\"enum\",\"name\":\"Strand\",\"doc\":\"Indicates the DNA strand associate for some data item.\\n* `NEG_STRAND`: The negative (-) strand.\\n* `POS_STRAND`: The postive (+) strand.\",\"symbols\":[\"NEG_STRAND\",\"POS_STRAND\"]},\"doc\":\"Strand the position is associated with.\"}]},\"doc\":\"The position of this alignment.\"},{\"name\":\"mappingQuality\",\"type\":[\"null\",\"int\"],\"doc\":\"The mapping quality of this alignment, meaning the likelihood that the read\\n maps to this position.\\n\\n Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the\\n nearest integer.\",\"default\":null},{\"name\":\"cigar\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"CigarUnit\",\"doc\":\"A structure for an instance of a CIGAR operation.\\n`FIXME: This belongs under Reads (only readAlignment refers to this)`\",\"fields\":[{\"name\":\"operation\",\"type\":{\"type\":\"enum\",\"name\":\"CigarOperation\",\"doc\":\"An enum for the different types of CIGAR alignment operations that exist.\\nUsed wherever CIGAR alignments are used. The different enumerated values\\nhave the following usage:\\n\\n* `ALIGNMENT_MATCH`: An alignment match indicates that a sequence can be\\n aligned to the reference without evidence of an INDEL. Unlike the\\n `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, the `ALIGNMENT_MATCH`\\n operator does not indicate whether the reference and read sequences are an\\n exact match. This operator is equivalent to SAM's `M`.\\n* `INSERT`: The insert operator indicates that the read contains evidence of\\n bases being inserted into the reference. This operator is equivalent to\\n SAM's `I`.\\n* `DELETE`: The delete operator indicates that the read contains evidence of\\n bases being deleted from the reference. This operator is equivalent to\\n SAM's `D`.\\n* `SKIP`: The skip operator indicates that this read skips a long segment of\\n the reference, but the bases have not been deleted. This operator is\\n commonly used when working with RNA-seq data, where reads may skip long\\n segments of the reference between exons. This operator is equivalent to\\n SAM's 'N'.\\n* `CLIP_SOFT`: The soft clip operator indicates that bases at the start/end\\n of a read have not been considered during alignment. This may occur if the\\n majority of a read maps, except for low quality bases at the start/end of\\n a read. This operator is equivalent to SAM's 'S'. Bases that are soft clipped\\n will still be stored in the read.\\n* `CLIP_HARD`: The hard clip operator indicates that bases at the start/end of\\n a read have been omitted from this alignment. This may occur if this linear\\n alignment is part of a chimeric alignment, or if the read has been trimmed\\n (e.g., during error correction, or to trim poly-A tails for RNA-seq). This\\n operator is equivalent to SAM's 'H'.\\n* `PAD`: The pad operator indicates that there is padding in an alignment.\\n This operator is equivalent to SAM's 'P'.\\n* `SEQUENCE_MATCH`: This operator indicates that this portion of the aligned\\n sequence exactly matches the reference (e.g., all bases are equal to the\\n reference bases). This operator is equivalent to SAM's '='.\\n* `SEQUENCE_MISMATCH`: This operator indicates that this portion of the\\n aligned sequence is an alignment match to the reference, but a sequence\\n mismatch (e.g., the bases are not equal to the reference). This can\\n indicate a SNP or a read error. This operator is equivalent to SAM's 'X'.\",\"symbols\":[\"ALIGNMENT_MATCH\",\"INSERT\",\"DELETE\",\"SKIP\",\"CLIP_SOFT\",\"CLIP_HARD\",\"PAD\",\"SEQUENCE_MATCH\",\"SEQUENCE_MISMATCH\"]},\"doc\":\"The operation type.\"},{\"name\":\"operationLength\",\"type\":\"long\",\"doc\":\"The number of bases that the operation runs for.\"},{\"name\":\"referenceSequence\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"`referenceSequence` is only used at mismatches (`SEQUENCE_MISMATCH`)\\n and deletions (`DELETE`). Filling this field replaces the MD tag.\\n If the relevant information is not available, leave this field as `null`.\",\"default\":null}]}},\"doc\":\"Represents the local alignment of this sequence (alignment matches, indels, etc)\\n versus the reference.\",\"default\":[]}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** The position of this alignment. */
private org.ga4gh.models.Position position;
/** The mapping quality of this alignment, meaning the likelihood that the read
maps to this position.
Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the
nearest integer. */
private java.lang.Integer mappingQuality;
/** Represents the local alignment of this sequence (alignment matches, indels, etc)
versus the reference. */
private java.util.List cigar;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public LinearAlignment() {}
/**
* All-args constructor.
*/
public LinearAlignment(org.ga4gh.models.Position position, java.lang.Integer mappingQuality, java.util.List cigar) {
this.position = position;
this.mappingQuality = mappingQuality;
this.cigar = cigar;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return position;
case 1: return mappingQuality;
case 2: return cigar;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: position = (org.ga4gh.models.Position)value$; break;
case 1: mappingQuality = (java.lang.Integer)value$; break;
case 2: cigar = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'position' field.
* The position of this alignment. */
public org.ga4gh.models.Position getPosition() {
return position;
}
/**
* Sets the value of the 'position' field.
* The position of this alignment. * @param value the value to set.
*/
public void setPosition(org.ga4gh.models.Position value) {
this.position = value;
}
/**
* Gets the value of the 'mappingQuality' field.
* The mapping quality of this alignment, meaning the likelihood that the read
maps to this position.
Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the
nearest integer. */
public java.lang.Integer getMappingQuality() {
return mappingQuality;
}
/**
* Sets the value of the 'mappingQuality' field.
* The mapping quality of this alignment, meaning the likelihood that the read
maps to this position.
Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the
nearest integer. * @param value the value to set.
*/
public void setMappingQuality(java.lang.Integer value) {
this.mappingQuality = value;
}
/**
* Gets the value of the 'cigar' field.
* Represents the local alignment of this sequence (alignment matches, indels, etc)
versus the reference. */
public java.util.List getCigar() {
return cigar;
}
/**
* Sets the value of the 'cigar' field.
* Represents the local alignment of this sequence (alignment matches, indels, etc)
versus the reference. * @param value the value to set.
*/
public void setCigar(java.util.List value) {
this.cigar = value;
}
/** Creates a new LinearAlignment RecordBuilder */
public static org.ga4gh.models.LinearAlignment.Builder newBuilder() {
return new org.ga4gh.models.LinearAlignment.Builder();
}
/** Creates a new LinearAlignment RecordBuilder by copying an existing Builder */
public static org.ga4gh.models.LinearAlignment.Builder newBuilder(org.ga4gh.models.LinearAlignment.Builder other) {
return new org.ga4gh.models.LinearAlignment.Builder(other);
}
/** Creates a new LinearAlignment RecordBuilder by copying an existing LinearAlignment instance */
public static org.ga4gh.models.LinearAlignment.Builder newBuilder(org.ga4gh.models.LinearAlignment other) {
return new org.ga4gh.models.LinearAlignment.Builder(other);
}
/**
* RecordBuilder for LinearAlignment instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private org.ga4gh.models.Position position;
private java.lang.Integer mappingQuality;
private java.util.List cigar;
/** Creates a new Builder */
private Builder() {
super(org.ga4gh.models.LinearAlignment.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.ga4gh.models.LinearAlignment.Builder other) {
super(other);
if (isValidValue(fields()[0], other.position)) {
this.position = data().deepCopy(fields()[0].schema(), other.position);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.mappingQuality)) {
this.mappingQuality = data().deepCopy(fields()[1].schema(), other.mappingQuality);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.cigar)) {
this.cigar = data().deepCopy(fields()[2].schema(), other.cigar);
fieldSetFlags()[2] = true;
}
}
/** Creates a Builder by copying an existing LinearAlignment instance */
private Builder(org.ga4gh.models.LinearAlignment other) {
super(org.ga4gh.models.LinearAlignment.SCHEMA$);
if (isValidValue(fields()[0], other.position)) {
this.position = data().deepCopy(fields()[0].schema(), other.position);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.mappingQuality)) {
this.mappingQuality = data().deepCopy(fields()[1].schema(), other.mappingQuality);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.cigar)) {
this.cigar = data().deepCopy(fields()[2].schema(), other.cigar);
fieldSetFlags()[2] = true;
}
}
/** Gets the value of the 'position' field */
public org.ga4gh.models.Position getPosition() {
return position;
}
/** Sets the value of the 'position' field */
public org.ga4gh.models.LinearAlignment.Builder setPosition(org.ga4gh.models.Position value) {
validate(fields()[0], value);
this.position = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'position' field has been set */
public boolean hasPosition() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'position' field */
public org.ga4gh.models.LinearAlignment.Builder clearPosition() {
position = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'mappingQuality' field */
public java.lang.Integer getMappingQuality() {
return mappingQuality;
}
/** Sets the value of the 'mappingQuality' field */
public org.ga4gh.models.LinearAlignment.Builder setMappingQuality(java.lang.Integer value) {
validate(fields()[1], value);
this.mappingQuality = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'mappingQuality' field has been set */
public boolean hasMappingQuality() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'mappingQuality' field */
public org.ga4gh.models.LinearAlignment.Builder clearMappingQuality() {
mappingQuality = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'cigar' field */
public java.util.List getCigar() {
return cigar;
}
/** Sets the value of the 'cigar' field */
public org.ga4gh.models.LinearAlignment.Builder setCigar(java.util.List value) {
validate(fields()[2], value);
this.cigar = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'cigar' field has been set */
public boolean hasCigar() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'cigar' field */
public org.ga4gh.models.LinearAlignment.Builder clearCigar() {
cigar = null;
fieldSetFlags()[2] = false;
return this;
}
@Override
public LinearAlignment build() {
try {
LinearAlignment record = new LinearAlignment();
record.position = fieldSetFlags()[0] ? this.position : (org.ga4gh.models.Position) defaultValue(fields()[0]);
record.mappingQuality = fieldSetFlags()[1] ? this.mappingQuality : (java.lang.Integer) defaultValue(fields()[1]);
record.cigar = fieldSetFlags()[2] ? this.cigar : (java.util.List) defaultValue(fields()[2]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}