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CovariateKey.scala
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CovariateKey.scala
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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.bdgenomics.adam.ds.read.recalibration
/**
* Represents a tuple containing a value for each covariate.
*
* @param readGroupId The ID of the read group that bases in this error
* covariate came from.
* @param qualityScore The quality score of bases in this covariate.
* @param cycle The sequencer cycle that bases in this covariate came from.
* @param dinucPrev The nucleotide preceding this base.
* @param dinucCurr The nucleotide that was observed.
* @param shouldInclude Whether this base should be included in the
* recalibration table.
* @param isMismatch Whether this base was a mismatch against the reference.
*/
private[adam] case class CovariateKey(
readGroupId: Int,
qualityScore: Char,
cycle: Int,
dinucPrev: Char,
dinucCurr: Char,
shouldInclude: Boolean = true,
isMismatch: Boolean = false) {
/**
* @return Returns a new CovariateKey with the shouldInclude and isMismatch
* fields reset to their defaults.
*/
def toDefault: CovariateKey = {
copy(shouldInclude = true, isMismatch = false)
}
/**
* @return Returns true if either the observed or preceeding bases were 'N'.
*
* @note This is required to render CSV formatting that matches the GATK.
*/
def containsNone: Boolean = {
dinucPrev == 'N' && dinucCurr == 'N'
}
/**
* @return Packages the dinucleotide covariate as a tuple.
*/
def dinuc: (Char, Char) = {
(dinucPrev, dinucCurr)
}
}