From a3d1d49e602265ba80b27894ed38a88c64a4788d Mon Sep 17 00:00:00 2001
From: Frank Austin Nothaft <fnothaft@alumni.stanford.edu>
Date: Wed, 25 Jan 2017 00:53:36 -0800
Subject: [PATCH] Clean up some INDEL bits.

---
 .../genotyping/BiallelicGenotyper.scala        | 18 +++++++++++++++++-
 .../avocado/genotyping/DiscoverVariants.scala  |  6 +++++-
 .../avocado/genotyping/Observer.scala          | 10 +++++++---
 .../avocado/models/Observation.scala           | 18 ++++++++++++++++++
 4 files changed, 47 insertions(+), 5 deletions(-)

diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyper.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyper.scala
index 3011b521..125c05fa 100644
--- a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyper.scala
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyper.scala
@@ -259,10 +259,26 @@ private[avocado] object BiallelicGenotyper extends Serializable with Logging {
             } else if (isInsertion(variant)) {
               val insAllele = variant.getAlternateAllele.tail
               val insObserved = observed.filter(_._2 == insAllele)
+              println("for %s observed %s in %s".format(insAllele, observed.mkString(","), read))
               if (observed.size == 2 &&
                 insObserved.size == 1) {
                 Some((variant, insObserved.head._3.duplicate(Some(false))))
-              } else if (observed.forall(_._3.isRef)) {
+              } else if (!observed.forall(_._3.isRef)) {
+                val nonRef = observed.filter(!_._3.isRef)
+                if (nonRef.size == 1) {
+                  val (_, allele, nonRefObs) = nonRef.head
+                  if (allele.length == insAllele.length) {
+                    val matchingBases = allele.zip(insAllele).count(p => p._1 == p._2)
+                    Some((variant, nonRefObs.scale(matchingBases,
+                      insAllele.length,
+                      Some(false))))
+                  } else {
+                    Some((variant, observed.head._3.nullOut))
+                  }
+                } else {
+                  Some((variant, observed.head._3.nullOut))
+                }
+              } else if (read.getEnd != variant.getEnd) {
                 Some((variant, observed.head._3.invert))
               } else {
                 Some((variant, observed.head._3.nullOut))
diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/DiscoverVariants.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/DiscoverVariants.scala
index 11a46041..9b3acc4a 100644
--- a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/DiscoverVariants.scala
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/DiscoverVariants.scala
@@ -201,7 +201,11 @@ object DiscoverVariants extends Serializable with Logging {
               kv
             }
             case Insertion(length) => {
-              val insQuals = qual.substring(idx - 1, idx + length).map(_.toInt - 33).sum / length
+              val insQuals = if (length > 0) {
+                qual.substring(idx - 1, idx + length).map(_.toInt - 33).sum / length
+              } else {
+                0
+              }
               val newVar = if (insQuals >= phredThreshold) {
                 Variant.newBuilder
                   .setContigName(contigName)
diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/Observer.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/Observer.scala
index 144e7839..72e2f92d 100644
--- a/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/Observer.scala
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/Observer.scala
@@ -131,9 +131,13 @@ private[genotyping] object Observer extends Serializable {
 
         // get bases and quals
         val bases = readSequence.substring(oldReadIdx, readIdx)
-        val qual = readQualities.substring(oldReadIdx, readIdx)
-          .map(_.toInt - 33)
-          .sum / length
+        val qual = if (length > 0) {
+          readQualities.substring(oldReadIdx, readIdx)
+            .map(_.toInt - 33)
+            .sum / length
+        } else {
+          0
+        }
 
         // the key is the (site, allele, sampleId)
         // insertions associate to the site to their left, hence the -1
diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/models/Observation.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/models/Observation.scala
index 3cfcd653..eb1be137 100644
--- a/avocado-core/src/main/scala/org/bdgenomics/avocado/models/Observation.scala
+++ b/avocado-core/src/main/scala/org/bdgenomics/avocado/models/Observation.scala
@@ -91,6 +91,24 @@ case class Observation(alleleForwardStrand: Int,
       isRef = setRef.getOrElse(isRef))
   }
 
+  /**
+   * @return Makes a copy where underlying arrays are not shared.
+   */
+  def scale(num: Int,
+            denum: Int,
+            setRef: Option[Boolean] = None): Observation = {
+    val scaleBy = num.toDouble / denum.toDouble
+    Observation(alleleForwardStrand,
+      otherForwardStrand,
+      squareMapQ,
+      alleleLogLikelihoods.map(v => v * scaleBy),
+      otherLogLikelihoods.map(v => v * scaleBy),
+      alleleCoverage,
+      otherCoverage,
+      totalCoverage = totalCoverage,
+      isRef = setRef.getOrElse(isRef))
+  }
+
   /**
    * @return Returns this observation, but with allele/other swapped.
    *