VariantDB

db.VariantDB

All Implemented Interfaces and Traits:

java.io.Closeable
```
@groovy.util.logging.Log
class VariantDB
extends java.lang.Object
implements java.io.Closeable
```
VariantDB implements a simple, embedded, variant tracking database that can be used to track variants identified in multiple samples and sequencing runs. It allows quick computation of variant counts across samples, families, batches of samples, etc.
For the full power of the database, you shoudl use a PED file, parsed with the Pedigrees class when adding variants and samples. However this parameter can be passed as null, in which case all samples are treated as singletons. You should be aware that variant counts will not be family aware in such cases and thus will be distorted if your sequencing has large pedigrees and compared to the overall sample count.
To add variants, parse them using the VCF class and then simple use the #add method:
```
 VariantDB db = new VariantDB("test.db")
 VCF.parse("test.vcf") { v ->
     db.add("batch1", null, v)
 }
 
```
Authors:
simon

Properties Summary

Properties
Type	Name and description
`static java.lang.Object`	`ANNOVAR_ANNOTATION_PROFILE`
`java.util.Map<java.lang.String, java.util.List<java.lang.String>>`	`annotationProfile`
`java.util.Map<java.lang.String, java.lang.Object>`	`cachedSampleInfo` Map of string to database rows of cached sample information
`java.lang.String`	`connectString` The file name of the database that is connected to
`groovy.sql.Sql`	`db` The actual database connection
`java.lang.String`	`driver` The file name of the database that is connected to
`Schema`	`schema` Schema for database

Constructor Summary

Constructors
Constructor and description
`VariantDB (java.lang.String fileName)` Open or create a VariantDB using default settings and the given file name.

Methods Summary

Methods
Type Params	Return Type	Name and description
	`int`	`add(java.lang.String batch, Pedigrees peds, gngs.Variant v, gngs.Variant$Allele alleleToAdd, java.lang.String cohort, java.lang.String sampleToAdd, java.lang.Object annotations)` Add the given variant to the database.
	`java.util.Map`	`addCachedSampleInfo(java.util.List<java.lang.String> addSamples, java.lang.String batch, java.lang.String cohort, Pedigrees peds)` Returns cached rows from the sample table for each sample.
	`java.lang.Object`	`addSample(java.lang.String sampleId, Pedigrees peds, java.lang.String cohort, java.lang.String batch)` Add information about the given sample to the database
	`void`	`addSampleBatch(java.lang.Long sampleId, java.lang.String batch, java.lang.String cohort)`
	`void`	`close()`
	`java.util.Map`	`countObservations(java.lang.String chr, int start, int end, java.lang.String alt)` Returns a map containing the following keys: sampleCount - the number of unique samples in which the variant was observed familyCount - the number of unique families in which the variant was observed
	`java.util.Map`	`countObservations(gngs.Variant v, gngs.Variant$Allele allele, java.lang.String batch)` Return a counts of the number of observations of the given variant.
	`java.lang.Object`	`findSample(java.lang.String sampleId)` Return row of database representing sample, or null if it does not exist.
	`java.lang.Object`	`findVariant(gngs.Variant variant, gngs.Variant$Allele allele)` Find a variant in the database by its start position
	`java.lang.Object`	`getAnnotation(java.lang.String type, java.lang.Object annotations)` Search for the given value in the annotations as a frequency value.
	`java.lang.Float`	`getFreq(java.lang.String type, java.lang.Object annotations)` Search for the given value in the annotations as a frequency value.
	`void`	`init()` Check the database exists and upgrade it if necessary
	`static void`	`main(java.lang.String[] args)` Simple test program - all it does is creates the database
	`java.util.Map`	`queryVariantCounts(java.util.Map options, gngs.Variant variant, gngs.Variant$Allele allele, java.lang.String sampleId)` Return a set of counts of times the given variant has been observed with in
	`java.lang.String`	`trimSampleId(java.lang.String sampleId)`
	`void`	`tx(groovy.lang.Closure c)` Execute the given closure in teh scope of a transaction, and roll it back if an exception occurs.

Inherited Methods Summary

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

- Property Detail
  - static final java.lang.Object ANNOVAR_ANNOTATION_PROFILE
  - java.util.Map<java.lang.String, java.util.List<java.lang.String>> annotationProfile
  - java.util.Map<java.lang.String, java.lang.Object> cachedSampleInfo
    
    Map of string to database rows of cached sample information
  - java.lang.String connectString
    
    The file name of the database that is connected to
  - groovy.sql.Sql db
    
    The actual database connection
  - java.lang.String driver
    
    The file name of the database that is connected to
  - Schema schema
    
    Schema for database
- Constructor Detail
  - VariantDB(java.lang.String fileName)
    
    Open or create a VariantDB using default settings and the given file name. These connect to a SQLite database with the given name.
    Parameters:
    fileName
- Method Detail
  - int add(java.lang.String batch, Pedigrees peds, gngs.Variant v, gngs.Variant$Allele alleleToAdd, java.lang.String cohort, java.lang.String sampleToAdd, java.lang.Object annotations)
    
    Add the given variant to the database. If sampleToAdd is specified, add it for only the given sample. Otherwise add it for all the samples that are genotyped to have the variant
    Parameters:
    annotations - optional annotations to draw from. These can be used when the annotations are not embedded in the VCF file. The annotations are queried for keys defined in the annotationProfile field. The default mappings are set up to look for Annovar annotations. The annotations themselves can be any object having properties which will be queried. In practise, a CSV parser PropertyMapper is what is being used here to pass in Annovar annotations.
    Returns:
    count of variants added
  - java.util.Map addCachedSampleInfo(java.util.List<java.lang.String> addSamples, java.lang.String batch, java.lang.String cohort, Pedigrees peds)
    
    Returns cached rows from the sample table for each sample. If rows do not exist yet for the sample, adds rows to the table. If rows do exist, returns the existing rows. Also adds batch information.
    Parameters:
    addSamples
    batch
    cohort
    Returns:
    a map keyed on sample id, with values being the row from the sample table for each sample
  - java.lang.Object addSample(java.lang.String sampleId, Pedigrees peds, java.lang.String cohort, java.lang.String batch)
    
    Add information about the given sample to the database @return
    Parameters:
    sampleId
    peds
  - void addSampleBatch(java.lang.Long sampleId, java.lang.String batch, java.lang.String cohort)
  - void close()
  - java.util.Map countObservations(java.lang.String chr, int start, int end, java.lang.String alt)
    
    Returns a map containing the following keys:
  - sampleCount - the number of unique samples in which the variant was observed
  - familyCount - the number of unique families in which the variant was observed
    Parameters:
    chr - Chromosome of variant
    start - starting position of DNA change caused by variant (note this may be different to VCF position depending on the representation of your indel in the VCF!)
    end - end position of DNA change caused by variant
    alt - alternate sequence
    Returns:
    Map with keys indicating counts of observations of this variant
  - java.util.Map countObservations(gngs.Variant v, gngs.Variant$Allele allele, java.lang.String batch)
    
    Return a counts of the number of observations of the given variant. Two values are returned:
  - sampleCount - the number of unique samples in which the variant was observed
  - familyCount - the number of unique families in which the variant was observed
    Parameters:
    batch - If provided, variants will only be provided if they are observed in this batch OR any earlier batch. The intent is to support reproducibility so that new samples can be added to the database without changing the variant counts if queried for old samples.
  - java.lang.Object findSample(java.lang.String sampleId)
    
    Return row of database representing sample, or null if it does not exist.
  - java.lang.Object findVariant(gngs.Variant variant, gngs.Variant$Allele allele)
    
    Find a variant in the database by its start position
  - java.lang.Object getAnnotation(java.lang.String type, java.lang.Object annotations)
    
    Search for the given value in the annotations as a frequency value.
    Parameters:
    type - The type of value to search for, must be one of the predefined annotation profile keys
    annotations - The annotations to search
    Returns:
    the value of the annotation or null if it is not available
  - java.lang.Float getFreq(java.lang.String type, java.lang.Object annotations)
    
    Search for the given value in the annotations as a frequency value. @return
    Parameters:
    type - The type of frequency to search for, must be a key in the annotation profile
    annotations - The annotations to search
  - void init()
    
    Check the database exists and upgrade it if necessary
  - static void main(java.lang.String[] args)
    
    Simple test program - all it does is creates the database
    Parameters:
    args
  - java.util.Map queryVariantCounts(java.util.Map options, gngs.Variant variant, gngs.Variant$Allele allele, java.lang.String sampleId)
    
    Return a set of counts of times the given variant has been observed with in
  - all cohorts
  - all except the specified cohort
  - within the specified cohort Additional cohorts can be excluded by setting a comma separated list as the value 'excludeCohorts' in options.
    The returned map has 3 attributes:
  - total - total number of smaples observed to have the variant, regardless of cohort
  - in_target - total number of samples observed to have the variant within specified cohort
  - other_target - total number of samples observed to have the variant outside of specified cohort
  - java.lang.String trimSampleId(java.lang.String sampleId)
  - void tx(groovy.lang.Closure c)
    
    Execute the given closure in teh scope of a transaction, and roll it back if an exception occurs.
    Parameters:
    c - Closure to execute

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation

[Groovy] Class VariantDB

Properties Summary

Constructor Summary

Methods Summary

Inherited Methods Summary

Property Detail

static final java.lang.Object ANNOVAR_ANNOTATION_PROFILE

java.util.Map<java.lang.String, java.util.List<java.lang.String>> annotationProfile

java.util.Map<java.lang.String, java.lang.Object> cachedSampleInfo

java.lang.String connectString

groovy.sql.Sql db

java.lang.String driver

Schema schema

Constructor Detail

VariantDB(java.lang.String fileName)

Method Detail

int add(java.lang.String batch, Pedigrees peds, gngs.Variant v, gngs.Variant$Allele alleleToAdd, java.lang.String cohort, java.lang.String sampleToAdd, java.lang.Object annotations)

java.util.Map addCachedSampleInfo(java.util.List<java.lang.String> addSamples, java.lang.String batch, java.lang.String cohort, Pedigrees peds)

java.lang.Object addSample(java.lang.String sampleId, Pedigrees peds, java.lang.String cohort, java.lang.String batch)

void addSampleBatch(java.lang.Long sampleId, java.lang.String batch, java.lang.String cohort)

void close()

java.util.Map countObservations(java.lang.String chr, int start, int end, java.lang.String alt)

java.util.Map countObservations(gngs.Variant v, gngs.Variant$Allele allele, java.lang.String batch)

java.lang.Object findSample(java.lang.String sampleId)

java.lang.Object findVariant(gngs.Variant variant, gngs.Variant$Allele allele)

java.lang.Object getAnnotation(java.lang.String type, java.lang.Object annotations)

java.lang.Float getFreq(java.lang.String type, java.lang.Object annotations)

void init()

static void main(java.lang.String[] args)

java.util.Map queryVariantCounts(java.util.Map options, gngs.Variant variant, gngs.Variant$Allele allele, java.lang.String sampleId)

java.lang.String trimSampleId(java.lang.String sampleId)

void tx(groovy.lang.Closure c)