POC of a tool to re-pick primary alignments.

src/main/scala/com/fulcrumgenomics/bam/PickPrimaryAlignment.scala

@@ -0,0 +1,100 @@
+/*
+ * The MIT License
+ *
+ * Copyright (c) 2024 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.sopt.{arg, clp}
+import com.fulcrumgenomics.util.ProgressLogger
+
+@clp(group=ClpGroups.SamOrBam, description="""
+Resets which record is marked as the primary alignment per read.
+""")
+class PickPrimaryAlignment(
+  @arg(flag='i', doc="") val input: PathToBam,
+  @arg(flag='o', doc="") val output: PathToBam
+) extends FgBioTool {
+
+  override def execute(): Unit = {
+    val in       = SamSource(input)
+    val out      = SamWriter(output, in.header)
+    val progress = ProgressLogger(this.logger, noun="templates")
+
+    Bams.templateIterator(in).foreach { template =>
+      val fixed = pickPrimaries(template)
+      if (!(fixed eq template)) {
+        fixed.fixMateInfo()
+      }
+
+      out ++= fixed.allReads
+      progress.record()
+    }
+
+    in.safelyClose()
+    out.close()
+  }
+
+  /** Re-picks the primary mappings for any reads that have supplementary reads. */
+  private[bam] def pickPrimaries(t: Template): Template = {
+    if (t.r1Supplementals.isEmpty && t.r2Supplementals.isEmpty) {
+      t
+    }
+    else {
+      val r1Primary = if (t.r1Supplementals.isEmpty) t.r1 else {
+        Some(pickPrimary(t.r1 ++ t.r1Supplementals))
+      }
+      val r2Primary = if (t.r2Supplementals.isEmpty) t.r2 else {
+        Some(pickPrimary(t.r2 ++ t.r2Supplementals))
+      }
+
+      if ((r1Primary eq t.r1) && (r2Primary eq t.r2)) t else {
+        r1Primary.foreach(_.supplementary = false)
+        r2Primary.foreach(_.supplementary = false)
+
+        Template(
+          r1 = r1Primary,
+          r2 = r2Primary,
+          r1Supplementals = (t.r1 ++ t.r1Supplementals).filter(r => !r1Primary.exists(_ eq r)).tapEach(_.supplementary=true).toSeq,
+          r2Supplementals = (t.r2 ++ t.r2Supplementals).filter(r => !r2Primary.exists(_ eq r)).tapEach(_.supplementary=true).toSeq,
+          r1Secondaries   = t.r1Secondaries,
+          r2Secondaries   = t.r2Secondaries
+        )
+      }
+    }
+  }
+
+  /** Selects the record, among mappings of the same read, with the earliest query base aligned. */
+  private [bam] def pickPrimary(recs: Iterable[SamRecord]): SamRecord = {
+    recs.minBy(firstMappedBaseInQueryOrder)
+  }
+
+  /** Returns the 1-based position of the first query base that is aligned to the reference. */
+  private [bam] def firstMappedBaseInQueryOrder(rec: SamRecord): Int = {
+    require(rec.mapped, s"Record is unmapped: ${rec}")
+    val iter = (if (rec.negativeStrand) rec.cigar.elems.reverseIterator else rec.cigar.elems.iterator).bufferBetter
+    iter.takeWhile(!_.operator.isAlignment).sumBy(_.lengthOnQuery)
+  }
+}