Package org.broadinstitute.hellbender.utils.samples

package org.broadinstitute.hellbender.utils.samples
  • Class
    Description
    Affection
    Categorical sample trait for association and analysis Samples can have unknown status, be affected or unaffected by the categorical trait, or they can be marked as actually having an other trait value (stored in an associated value in the Sample class)
    MendelianViolation
    Class for the identification and tracking of mendelian violation.
    PedigreeValidationType
     
    PedReader
    Reads PED file-formatted tabular text files See http://www.broadinstitute.org/mpg/tagger/faq.html See http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped The "ped" file format refers to the widely-used format for linkage pedigree data.
    PedReader.Field
     
    PedReader.MissingPedField
    An enum that specifies which, if any, of the standard PED fields are missing from the input records.
    Sample
    Represents an individual under study.
    SampleDB
    Simple database for managing samples
    SampleDBBuilder
    Class for creating a temporary in memory database of samples.
    Sex
    ENUM of possible human sexes: male, female, or unknown
    Trio
    A class for imposing a trio structure on three samples; a common paradigm