A tool to regenerate the NM/UQ/MD tags on a SAM or BAM file Raw with logging

RegenerateNmUqMdTags.scala

package com.nilshomer.bfx.examples.utilities

import com.fulcrumgenomics.FgBioDef.PathToFasta
import com.fulcrumgenomics.bam.Bams
import com.fulcrumgenomics.bam.api.{SamOrder, SamSource, SamWriter}
import com.fulcrumgenomics.cmdline.ClpGroups
import com.fulcrumgenomics.commons.CommonsDef.{PathToBam, SafelyClosable}
import com.fulcrumgenomics.commons.util.LazyLogging
import com.fulcrumgenomics.sopt.{arg, clp}
import com.fulcrumgenomics.util.{Io, ProgressLogger}
import com.nilshomer.bfx.examples.cmdline.BfxExamplesTool
import htsjdk.samtools.reference.ReferenceSequenceFileWalker

@clp(
  description = "Regenerates the NM/UQ/MD tags on a SAM or BAM file.",
  group       = ClpGroups.Utilities
)
class RegenerateNmUqMdTags
( @arg(flag='i', doc="Input SAM or BAM file of aligned reads in coordinate order.") val input: PathToBam,
  @arg(flag='o', doc="Output SAM or BAM file.") val output: PathToBam,
  @arg(flag='r', doc="Reference sequence FASTA file.") val ref: PathToFasta
) extends BfxExamplesTool with LazyLogging {
  Io.assertReadable(input)
  Io.assertReadable(ref)
  Io.assertCanWriteFile(output)
  def execute(): Unit = {
    val in       = SamSource(this.input)
    val walker   = new ReferenceSequenceFileWalker(ref.toFile)
    val out      = SamWriter(output, in.header, ref=Some(ref))
    val progress = ProgressLogger(logger, unit=1e6.toInt)

    require(SamOrder(in.header).contains(SamOrder.Coordinate), "Input must be coordinate sorted")

    logger.info(s"Reading from $input")
    logger.info(s"Writing to $output")
    in.foreach { rec =>
      Bams.regenerateNmUqMdTags(rec, walker)
      out += rec
      progress.record(rec)
    }
    logger.info(s"Wrote ${progress.getCount} records")

    in.safelyClose()
    out.close()
  }
}

terminal.out

$java -Xmx2g -jar tools/target/scala-2.12/bfx-examples-tools.jar RegenerateNmUqMdTags -i in.bam -r hs38DH.fa -o out.bam
[2017/11/04 23:13:24 | BfxExamplesMain | Info] Executing RegenerateNmUqMdTags from bfx-examples version 0.1.0-SNAPSHOT as nhomer@Nils on JRE 1.8.0_66-b17 without snappy
[2017/11/04 23:13:24 | RegenerateNmUqMdTags | Info] Reading from in.bam
[2017/11/04 23:13:24 | RegenerateNmUqMdTags | Info] Writing to out.bam
[2017/11/04 23:13:42 | RegenerateNmUqMdTags | Info] processed     1,000,000 records.  Elapsed time: 00:00:18s.  Time for last 1,000,000:   17s.  Last read position: chr3:93,470,582
[2017/11/04 23:14:00 | SamWriter | Info] Wrote      2,000,000 records.  Elapsed time: 00:00:35s.  Time for last 2,000,000:   35s.  Last read position: chr6:127,749,553
[2017/11/04 23:14:00 | RegenerateNmUqMdTags | Info] processed     2,000,000 records.  Elapsed time: 00:00:35s.  Time for last 1,000,000:   17s.  Last read position: chr6:127,749,553
[2017/11/04 23:14:17 | RegenerateNmUqMdTags | Info] processed     3,000,000 records.  Elapsed time: 00:00:52s.  Time for last 1,000,000:   16s.  Last read position: chr9:130,862,720
[2017/11/04 23:14:30 | SamWriter | Info] Wrote      4,000,000 records.  Elapsed time: 00:01:05s.  Time for last 2,000,000:   29s.  Last read position: chr9:130,872,057
[2017/11/04 23:14:30 | RegenerateNmUqMdTags | Info] processed     4,000,000 records.  Elapsed time: 00:01:05s.  Time for last 1,000,000:   13s.  Last read position: chr9:130,872,057
[2017/11/04 23:14:42 | RegenerateNmUqMdTags | Info] processed     5,000,000 records.  Elapsed time: 00:01:18s.  Time for last 1,000,000:   12s.  Last read position: chr9:130,874,801
[2017/11/04 23:14:55 | SamWriter | Info] Wrote      6,000,000 records.  Elapsed time: 00:01:30s.  Time for last 2,000,000:   24s.  Last read position: chr9:130,878,519
[2017/11/04 23:14:55 | RegenerateNmUqMdTags | Info] processed     6,000,000 records.  Elapsed time: 00:01:30s.  Time for last 1,000,000:   12s.  Last read position: chr9:130,878,519
[2017/11/04 23:15:07 | RegenerateNmUqMdTags | Info] processed     7,000,000 records.  Elapsed time: 00:01:43s.  Time for last 1,000,000:   12s.  Last read position: chr9:134,837,505
[2017/11/04 23:15:25 | SamWriter | Info] Wrote      8,000,000 records.  Elapsed time: 00:02:00s.  Time for last 2,000,000:   30s.  Last read position: chr14:86,718,794
[2017/11/04 23:15:25 | RegenerateNmUqMdTags | Info] processed     8,000,000 records.  Elapsed time: 00:02:00s.  Time for last 1,000,000:   17s.  Last read position: chr14:86,718,794
[2017/11/04 23:15:42 | RegenerateNmUqMdTags | Info] processed     9,000,000 records.  Elapsed time: 00:02:17s.  Time for last 1,000,000:   17s.  Last read position: chr22:32,161,343
[2017/11/04 23:15:46 | RegenerateNmUqMdTags | Info] Wrote 9216420 records
[2017/11/04 23:15:47 | BfxExamplesMain | Info] RegenerateNmUqMdTags completed. Elapsed time: 2.40 minutes.