feat: allow TrimFastq to specify a length per input FASTQ

See: #927

src/main/scala/com/fulcrumgenomics/fastq/TrimFastq.scala

@@ -46,26 +46,29 @@ import com.fulcrumgenomics.sopt._
 class TrimFastq
 (   @arg(flag='i', doc="One or more input fastq files.") val input:  Seq[PathToFastq],
     @arg(flag='o', doc="A matching number of output fastq files.") val output: Seq[PathToFastq],
-    @arg(flag='l', doc="Length to trim reads to.")             val length: Int,
+    @arg(flag='l', doc="Length to trim reads to (either one per input fastq file, or one for all).") val length: Seq[Int],
     @arg(flag='x', doc="Exclude reads below the trim length.") val exclude: Boolean = false
 ) extends FgBioTool with LazyLogging {
 
   validate(input.size == output.size, "Number of input and output files must match.")
+  validate(length.size == 1 || input.size == length.size, "Number of lengths must be one or match the number of input files.")
 
   override def execute(): Unit = {
     var discarded: Long = 0
     val progress = new ProgressLogger(this.logger, noun="records", verb="Wrote")
 
+    val lengths = if (this.length.size == 1) List.fill(this.input.size)(this.length.head) else this.length
+
     val sources = input.map(FastqSource(_))
     val writers = output.map(FastqWriter(_))
     while (allHaveNext(sources)) {
       val recs = sources.map(_.next())
-      if (exclude && recs.exists(_.length < length)) {
+      if (exclude && recs.zip(lengths).exists { case (rec, length) => rec.length < length }) {
         discarded += 1
       }
       else {
-        writers.iterator.zip(recs.iterator).foreach { case(w, r) =>
-          w.write(r.trimmedTo(length))
+        writers.lazyZip(recs).lazyZip(lengths).foreach { case (w: FastqWriter, r: FastqRecord, l: Int) =>
+          w.write(r.trimmedTo(l))
           progress.record()
         }
       }

src/test/scala/com/fulcrumgenomics/fastq/TrimFastqTest.scala

@@ -59,9 +59,9 @@ class TrimFastqTest extends UnitSpec {
   }
 
   "TrimFastq" should "trim a single file and not discard any records" in {
-    val (r1, r2) = fqFiles
+    val (r1, _) = fqFiles
     val out = makeTempFile("trimmed.", ".fq")
-    new TrimFastq(input=Seq(r1), output=Seq(out), length=15, exclude=false).execute()
+    new TrimFastq(input=Seq(r1), output=Seq(out), length=Seq(15), exclude=false).execute()
     val r1Map = FastqSource(out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 3
     r1Map("10x10").length shouldBe 10
@@ -70,18 +70,18 @@ class TrimFastqTest extends UnitSpec {
   }
 
   it should "trim a single file and discard 2 records" in {
-    val (r1, r2) = fqFiles
+    val (r1, _) = fqFiles
     val out = makeTempFile("trimmed.", ".fq")
-    new TrimFastq(input=Seq(r1), output=Seq(out), length=15, exclude=true).execute()
+    new TrimFastq(input=Seq(r1), output=Seq(out), length=Seq(15), exclude=true).execute()
     val r1Map = FastqSource(out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 1
     r1Map("20x20").length shouldBe 15
   }
 
   it should "trim a single file and discard 0 records because they are all long enough" in {
-    val (r1, r2) = fqFiles
+    val (r1, _) = fqFiles
     val out = makeTempFile("trimmed.", ".fq")
-    new TrimFastq(input=Seq(r1), output=Seq(out), length=5, exclude=true).execute()
+    new TrimFastq(input=Seq(r1), output=Seq(out), length=Seq(5), exclude=true).execute()
     val r1Map = FastqSource(out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 3
     r1Map("10x10").length shouldBe 5
@@ -92,7 +92,7 @@ class TrimFastqTest extends UnitSpec {
   it should "not trim or discard any reads" in {
     val (r1, r2) = fqFiles
     val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
-    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=25, exclude=false).execute()
+    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=Seq(25), exclude=false).execute()
     val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
     val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 3
@@ -108,7 +108,7 @@ class TrimFastqTest extends UnitSpec {
   it should "trim but not discard some reads" in {
     val (r1, r2) = fqFiles
     val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
-    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=15, exclude=false).execute()
+    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=Seq(15), exclude=false).execute()
     val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
     val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 3
@@ -124,12 +124,28 @@ class TrimFastqTest extends UnitSpec {
   it should "trim some reads and discard others by pair in" in {
     val (r1, r2) = fqFiles
     val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
-    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=15, exclude=true).execute()
+    new TrimFastq(input=Seq(r1, r2), output=Seq(r1Out, r2Out), length=Seq(15), exclude=true).execute()
     val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
     val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
     r1Map.size shouldBe 1
     r2Map.size shouldBe r1Map.size
     r1Map("20x20").length shouldBe 15
     r2Map("20x20").length shouldBe 15
   }
+
+  it should "trim some reads and discard others with FASTQ specific lengths" in {
+    val (r1, r2) = fqFiles
+    val (r1Out, r2Out) = (makeTempFile("r1out.", ".fq"), makeTempFile("r2out.", ".fq"))
+    new TrimFastq(input = Seq(r1, r2), output=Seq(r1Out, r2Out), length = Seq(10, 15), exclude = false).execute()
+    val r1Map = FastqSource(r1Out).map(r => r.name -> r).toMap
+    val r2Map = FastqSource(r2Out).map(r => r.name -> r).toMap
+    r1Map.size shouldBe 3
+    r2Map.size shouldBe r1Map.size
+    r1Map("10x10").length shouldBe 10
+    r1Map("10x20").length shouldBe 10
+    r1Map("20x20").length shouldBe 10
+    r2Map("10x10").length shouldBe 10
+    r2Map("10x20").length shouldBe 15
+    r2Map("20x20").length shouldBe 15
+  }
 }