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com.fulcrumgenomics.bam.pileup.RandomAccessPileupBuilder.scala Maven / Gradle / Ivy
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/*
* The MIT License
*
* Copyright (c) 2017 Fulcrum Genomics LLC
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.fulcrumgenomics.bam.pileup
import com.fulcrumgenomics.bam.api.QueryType.Overlapping
import com.fulcrumgenomics.bam.api.SamSource
import com.fulcrumgenomics.bam.pileup.PileupBuilder._
import com.fulcrumgenomics.fasta.SequenceDictionary
import java.io.Closeable
/** Companion object for [[RandomAccessPileupBuilder]]. */
object RandomAccessPileupBuilder {
/** Build a random access pileup builder from an indexed SAM source. */
def apply(
source: SamSource,
minMapQ: Int = PileupDefaults.minMapQ,
minBaseQ: Int = PileupDefaults.minBaseQ,
mappedPairsOnly: Boolean = PileupDefaults.mappedPairsOnly,
includeDuplicates: Boolean = PileupDefaults.includeDuplicates,
includeSecondaryAlignments: Boolean = PileupDefaults.includeSecondaryAlignments,
includeSupplementalAlignments: Boolean = PileupDefaults.includeSupplementalAlignments,
includeMapPositionsOutsideFrInsert: Boolean = PileupDefaults.includeMapPositionsOutsideFrInsert,
): RandomAccessPileupBuilder = {
require(source.indexed, "SAM source must be indexed for random access!")
new RandomAccessPileupBuilder(
source = source,
minMapQ = minMapQ,
minBaseQ = minBaseQ,
mappedPairsOnly = mappedPairsOnly,
includeDuplicates = includeDuplicates,
includeSecondaryAlignments = includeSecondaryAlignments,
includeSupplementalAlignments = includeSupplementalAlignments,
includeMapPositionsOutsideFrInsert = includeMapPositionsOutsideFrInsert,
)
}
}
/** A pileup builder that builds pileups using index-based BAM random access.
*
* @param source the indexed [[SamSource]] of records we will pileup.
* @param minBaseQ the minimum base quality that a base must have to contribute to a pileup.
* @param minMapQ the minimum mapping quality a record must have to contribute to a pileup.
* @param mappedPairsOnly if true, only allow paired records with both records mapped to contribute to a pileup.
* @param includeDuplicates if true, allow records flagged as duplicates to contribute to a pileup.
* @param includeSecondaryAlignments if true, allow records flagged as secondary alignments to contribute to a pileup.
* @param includeSupplementalAlignments if true, allow records flagged as supplementary alignments to contribute to a pileup.
* @param includeMapPositionsOutsideFrInsert if true, include any record of an FR pair where the site requested is outside the insert.
*/
class RandomAccessPileupBuilder private(
source: SamSource,
override val minMapQ: Int = PileupDefaults.minMapQ,
override val minBaseQ: Int = PileupDefaults.minBaseQ,
override val mappedPairsOnly: Boolean = PileupDefaults.mappedPairsOnly,
override val includeDuplicates: Boolean = PileupDefaults.includeDuplicates,
override val includeSecondaryAlignments: Boolean = PileupDefaults.includeSecondaryAlignments,
override val includeSupplementalAlignments: Boolean = PileupDefaults.includeSupplementalAlignments,
override val includeMapPositionsOutsideFrInsert: Boolean = PileupDefaults.includeMapPositionsOutsideFrInsert,
) extends PileupBuilder with Closeable {
/** The sequence dictionary associated with the records we will pileup. */
override val dict: SequenceDictionary = source.dict
/** Pileup records at this position. */
override def pileup(refName: String, pos: Int): Pileup[PileupEntry] = {
val end = Math.min(pos + 1, dict(refName).length) // Add 1bp to "end" in case a read has an insertion there.
val overlapping = source.query(refName, start = pos, end = end, Overlapping)
this.build(overlapping, refName = refName, pos = pos)
}
/** Close the wrapped SAM source. */
override def close(): Unit = source.close()
}
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