Add an entrypoint to SamSource for bytes of SAM/BAM/CRAM

src/main/scala/com/fulcrumgenomics/bam/api/SamSource.scala

@@ -24,48 +24,73 @@
 
 package com.fulcrumgenomics.bam.api
 
-import java.io.Closeable
-
 import com.fulcrumgenomics.FgBioDef._
 import com.fulcrumgenomics.bam.api.QueryType.QueryType
 import htsjdk.samtools._
 import htsjdk.samtools.util.{Interval, Locatable}
 
+import java.io.{Closeable, InputStream}
 import scala.collection.compat._
 
 /** Companion to the [[SamSource]] class that provides factory methods for sources. */
 object SamSource {
   var DefaultUseAsyncIo: Boolean = false
   var DefaultValidationStringency: ValidationStringency = ValidationStringency.STRICT
 
-  /**
-    * Constructs a [[SamSource]] to read from the provided path.
+  /** Configure a [[SAMRecordFactory]] with a variety of parameters. */
+  private def buildSamRecordFactory(
+    factory: SAMRecordFactory,
+    ref: Option[PathToFasta],
+    async: Boolean,
+    stringency: ValidationStringency,
+  ): SamReaderFactory = {
+    val fac = SamReaderFactory.make()
+    fac.samRecordFactory(factory)
+    fac.setUseAsyncIo(async)
+    fac.validationStringency(stringency)
+    ref.foreach(fac.referenceSequence)
+    fac
+  }
+
+  /** Constructs a [[SamSource]] to read from the provided path.
     *
     * @param path the path to read the SAM/BAM/CRAM from
     * @param index an optional path to read the index from
-    * @param ref an optional reference sequencing for decoding CRAM files
+    * @param ref an optional reference sequence for decoding CRAM files
     * @param async if true use extra thread(s) to speed up reading
     * @param stringency the validation stringency to apply when reading the data
-    * @param factory a SAMRecordFactory; MUST return classes that mix in [[SamRecord]]
+    * @param factory a [[SAMRecordFactory]]; MUST return classes that mix in [[SamRecord]]
     */
   def apply(path: PathToBam,
             index: Option[FilePath] = None,
             ref: Option[PathToFasta] = None,
             async: Boolean = DefaultUseAsyncIo,
             stringency: ValidationStringency = DefaultValidationStringency,
             factory: SAMRecordFactory = SamRecord.Factory): SamSource = {
-    // Configure the factory
-    val fac = SamReaderFactory.make()
-    fac.samRecordFactory(factory)
-    fac.setUseAsyncIo(async)
-    fac.validationStringency(stringency)
-    ref.foreach(r => fac.referenceSequence(r.toFile))
-
-    // Open the input(s)
+    val fac   = buildSamRecordFactory(factory = factory, ref = ref, async = async, stringency = stringency)
     val input = SamInputResource.of(path)
-    index.foreach(i => input.index(i))
+    index.foreach(input.index)
     new SamSource(fac.open(input))
   }
+
+  /** Constructs a [[SamSource]] to read from the provided input stream.
+    *
+    * @param stream the input stream of SAM/BAM/CRAM bytes
+    * @param ref an optional reference sequence for decoding CRAM files
+    * @param async if true use extra thread(s) to speed up reading
+    * @param stringency the validation stringency to apply when reading the data
+    * @param factory a [[SAMRecordFactory]]; MUST return classes that mix in [[SamRecord]]
+    */
+  def apply(
+    stream: InputStream,
+    ref: Option[PathToFasta],
+    async: Boolean,
+    stringency: ValidationStringency,
+    factory: SAMRecordFactory,
+  ): SamSource = {
+    val fac = buildSamRecordFactory(factory = factory, ref = ref, async = async, stringency = stringency)
+    new SamSource(fac.open(SamInputResource.of(stream)), closer = Some(() => stream.close()))
+  }
 }
 
 /** Describes the two types of queries that can be performed. */
@@ -78,7 +103,9 @@ object QueryType extends Enumeration {
   * A source class for reading SAM/BAM/CRAM files and for querying them.
   * @param reader the underlying [[SamReader]]
   */
-class SamSource private(private val reader: SamReader) extends View[SamRecord] with HeaderHelper with Closeable {
+class SamSource private(private val reader: SamReader, private val closer: Option[Closeable] = None)
+  extends View[SamRecord] with HeaderHelper with Closeable {
+
   /** The [[htsjdk.samtools.SAMFileHeader]] associated with the source. */
   override val header: SAMFileHeader = reader.getFileHeader
 
@@ -109,7 +136,11 @@ class SamSource private(private val reader: SamReader) extends View[SamRecord] w
   /** Provides a string that shows where the source is reading from. */
   override def toString: String = s"SamReader(${reader.getResourceDescription})"
 
-  override def close(): Unit = this.reader.close()
+  /** Close an optional wrapped closeable and release the SAM reader. */
+  override def close(): Unit = {
+    this.closer.foreach(_.close())
+    this.reader.close()
+  }
 
   /**
     * Returns the underlying SamReader. This should be avoided as much as possible, and the

src/test/scala/com/fulcrumgenomics/bam/api/SamIoTest.scala

@@ -24,15 +24,15 @@
 
 package com.fulcrumgenomics.bam.api
 
-import java.nio.file.Files
-import java.util.concurrent.{Callable, Executors, TimeUnit}
-
 import com.fulcrumgenomics.FgBioDef._
+import com.fulcrumgenomics.bam.api.SamSource.{DefaultUseAsyncIo, DefaultValidationStringency}
 import com.fulcrumgenomics.fasta.{SequenceDictionary, SequenceMetadata}
 import com.fulcrumgenomics.testing.{SamBuilder, UnitSpec}
 import com.fulcrumgenomics.util.Io
 import htsjdk.samtools.GenomicIndexUtil
 
+import java.nio.file.Files
+import java.util.concurrent.{Callable, Executors, TimeUnit}
 import scala.util.Random
 
 class SamIoTest extends UnitSpec {
@@ -164,4 +164,29 @@ class SamIoTest extends UnitSpec {
     filterCount shouldBe 10
     mapCount shouldBe 10
   }
+
+  it should "allow reading from a stream of SAM bytes" in {
+    val builder = new SamBuilder()
+    builder.addPair(name = "q1", start1 = 100, start2 = 300)
+    builder.addPair(name = "q4", start1 = 200, start2 = 400)
+    builder.addPair(name = "q3", start1 = 300, start2 = 500)
+    builder.addPair(name = "q2", start1 = 400, start2 = 600)
+
+    val sam = makeTempFile(getClass.getSimpleName, ".sam")
+    val out = SamWriter(sam, builder.header, sort = Some(SamOrder.Coordinate))
+    builder.foreach(out.write)
+    out.close()
+
+    val source = SamSource(
+      stream     = Io.toInputStream(sam),
+      ref        = None,
+      async      = DefaultUseAsyncIo,
+      stringency = DefaultValidationStringency,
+      factory    = SamRecord.Factory
+    )
+
+    source.indexed shouldBe false
+    source.toSeq.map(_.start) should contain theSameElementsInOrderAs Seq(100, 200, 300, 300, 400, 400, 500, 600)
+    source.close()
+  }
 }