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Performance improvements to SAM reading and processing #2280

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merged 2 commits into from
Nov 5, 2020
Merged

Performance improvements to SAM reading and processing #2280

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e0be1d8
Performance fixes to sam reading and processing
Nov 4, 2020
a246cf8
correct implementation of toString in SequenceDictionary
Nov 4, 2020
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14 changes: 9 additions & 5 deletions adam-core/src/main/scala/org/bdgenomics/adam/models/Attribute.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -36,16 +36,20 @@ case class Attribute(tag: String, tagType: TagType.Value, value: Any) {
val byteSequenceTypes = Array(TagType.NumericByteSequence, TagType.NumericUnsignedByteSequence)
val intSequenceTypes = Array(TagType.NumericIntSequence, TagType.NumericUnsignedIntSequence)
val shortSequenceTypes = Array(TagType.NumericShortSequence, TagType.NumericUnsignedShortSequence)
val sb = new StringBuilder
sb.append(tag)
sb.append(":")
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These could be all one line for code style purposes, but I don't mind either way

sb.append(tagType)
if (byteSequenceTypes contains tagType) {
"%s:%s,%s".format(tag, tagType, value.asInstanceOf[Array[Byte]].mkString(","))
sb.append(",").append(value.asInstanceOf[Array[Byte]].mkString(",")).toString()
} else if (shortSequenceTypes contains tagType) {
"%s:%s,%s".format(tag, tagType, value.asInstanceOf[Array[Short]].mkString(","))
sb.append(",").append(value.asInstanceOf[Array[Short]].mkString(",")).toString()
} else if (intSequenceTypes contains tagType) {
"%s:%s,%s".format(tag, tagType, value.asInstanceOf[Array[Int]].mkString(","))
sb.append(",").append(value.asInstanceOf[Array[Int]].mkString(",")).toString()
} else if (tagType == TagType.NumericFloatSequence) {
"%s:%s,%s".format(tag, tagType, value.asInstanceOf[Array[Float]].mkString(","))
sb.append(",").append(value.asInstanceOf[Array[Float]].mkString(",")).toString()
} else {
"%s:%s:%s".format(tag, tagType, value.toString)
sb.append(":").append(value).toString()
}
}
}
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4 changes: 2 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
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Expand Up @@ -184,7 +184,7 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
* @return Returns a SAM formatted sequence dictionary.
*/
def toSAMSequenceDictionary: SAMSequenceDictionary = {
new SAMSequenceDictionary(records.iterator.map(_.toSAMSequenceRecord).toList)
new SAMSequenceDictionary(records.map(_.toSAMSequenceRecord).asJava)
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This is a good catch, did you have profiling results leading you here, or were you able to eyeball it?

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Profiler, of course!

}

/**
Expand Down Expand Up @@ -259,7 +259,7 @@ class SequenceDictionary(val records: Vector[SequenceRecord]) extends Serializab
}

override def toString: String = {
records.map(_.toString).fold("SequenceDictionary{")(_ + "\n" + _) + "}"
records.map(_.toString).mkString("SequenceDictionary{", "\n", "}")
}

private[adam] def toAvro: Seq[Reference] = {
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