com.fulcrumgenomics.bam.SetMateInformation.scala Maven / Gradle / Ivy

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/*
 * The MIT License
 *
 * Copyright (c) 2016 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

import com.fulcrumgenomics.FgBioDef._
import com.fulcrumgenomics.bam.api.{SamRecord, SamSource, SamWriter}
import com.fulcrumgenomics.cmdline.{ClpGroups, FgBioTool}
import com.fulcrumgenomics.commons.util.LazyLogging
import com.fulcrumgenomics.sopt.cmdline.ValidationException
import com.fulcrumgenomics.sopt.{arg, clp}
import com.fulcrumgenomics.util.Io
import htsjdk.samtools.SAMFileHeader.{GroupOrder, SortOrder}
import htsjdk.samtools.SamPairUtil.SetMateInfoIterator

@clp(group=ClpGroups.SamOrBam, description=
"""
  |Adds and/or fixes mate information on paired-end reads. Sets the MQ (mate mapping quality),
  |`MC` (mate cigar string), ensures all mate-related flag fields are set correctly, and that
  |the mate reference and mate start position are correct.
  |
  |Supplementary records are handled correctly (updated with their mate's non-supplemental
  |attributes).  Secondary alignments are passed through but are not updated.
  |
  |The input file must be query-name sorted or query-name grouped (i.e. all records from the same
  |query sequence must be adjacent in the file, though the ordering between queries is unspecified).
""")
class SetMateInformation
(
  @arg(flag='i', doc="Input SAM/BAM/CRAM file.")                      val input: PathToBam = Io.StdIn,
  @arg(flag='o', doc="Output SAM/BAM/CRAM file.")                     val output: PathToBam = Io.StdOut,
  @arg(flag='r', doc="Reference fasta, only needed if writing CRAM.") val ref: Option[PathToFasta] = None,
  @arg(flag='x', doc="If specified, do not fail when reads marked as paired are missing their mate pairs.")
                                                                      val allowMissingMates: Boolean = false
) extends FgBioTool with LazyLogging {

  Io.assertReadable(input)
  Io.assertCanWriteFile(output)
  private val in = SamSource(input)
  if (in.header.getSortOrder != SortOrder.queryname && in.header.getGroupOrder != GroupOrder.query) {
    in.safelyClose()
    throw new ValidationException("Input is not queryname sorted or grouped.")
  }

  override def execute(): Unit = {
    val out = SamWriter(output, in.header, ref=ref)
    val iterator = new SetMateInfoIterator(in.iterator.map(_.asSam), true, allowMissingMates).map(_.asInstanceOf[SamRecord])
    out ++= iterator
    out.close()
    in.safelyClose()
  }
}