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[ADAM-369] Improve debug output for indel realigner #369

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Sep 16, 2014
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[ADAM-369] Improve debug output for indel realigner #369

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17 changes: 13 additions & 4 deletions adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ import scala.collection.immutable.{ NumericRange, TreeSet }
import scala.collection.mutable
import scala.util.Random

private[rdd] object RealignIndels {
private[rdd] object RealignIndels extends Serializable with Logging {

/**
* Realigns an RDD of reads.
Expand Down Expand Up @@ -181,9 +181,17 @@ private[rdd] object RealignIndels {
* From a set of reads, returns the reference sequence that they overlap.
*/
def getReferenceFromReads(reads: Iterable[RichAlignmentRecord]): (String, Long, Long) = {
var tossedReads = 0

// get reference and range from a single read
val readRefs = reads.map((r: RichAlignmentRecord) => {
(r.mdTag.get.getReference(r), r.getStart.toLong to r.getEnd)
val readRefs = reads.flatMap((r: RichAlignmentRecord) => {
if (r.mdTag.isDefined) {
Some((r.mdTag.get.getReference(r), r.getStart.toLong to r.getEnd))
} else {
log.warn("Discarding read " + r.record.getReadName + " during reference re-creation.")
tossedReads += 1
None
}
})
.toSeq
.sortBy(_._2.head)
Expand All @@ -196,7 +204,8 @@ private[rdd] object RealignIndels {
(reference._1 + refReads._1.substring((reference._2 - refReads._2.head).toInt), refReads._2.end)
} else {
// there is a gap in the sequence
throw new IllegalArgumentException("Current sequence has a gap at " + reference._2 + "with " + refReads._2.head + "," + refReads._2.end + ".")
throw new IllegalArgumentException("Current sequence has a gap at " + reference._2 + "with " + refReads._2.head + "," + refReads._2.end +
". Discarded " + tossedReads + " in region when reconstructing region; reads may not have MD tag attached.")
}
})

Expand Down