LociConversions

hammerlab · Feb 3, 2017 · b5429f8 · b5429f8
1 parent 1445521
commit b5429f8
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Showing 3 changed files with 42 additions and 41 deletions.
diff --git a/src/test/scala/org/hammerlab/genomics/reads/MappedReadSerializerSuite.scala b/src/test/scala/org/hammerlab/genomics/reads/MappedReadSerializerSuite.scala
@@ -1,7 +1,7 @@
 package org.hammerlab.genomics.reads
 
 import org.hammerlab.genomics.cigar._
-import org.hammerlab.genomics.reference.test.LocusUtil._
+import org.hammerlab.genomics.reference.test.LociConversions._
 
 class MappedReadSerializerSuite
   extends ReadSerializerSuite {

diff --git a/src/test/scala/org/hammerlab/genomics/reads/MappedReadSuite.scala b/src/test/scala/org/hammerlab/genomics/reads/MappedReadSuite.scala
@@ -3,56 +3,58 @@ package org.hammerlab.genomics.reads
 import htsjdk.samtools.{ SAMFileHeader, SAMRecord, TextCigarCodec }
 import org.hammerlab.genomics.bases.BasesUtil
 import org.hammerlab.genomics.cigar.makeCigar
-import org.hammerlab.genomics.reference.test.LocusUtil
+import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.test.Suite
 
 class MappedReadSuite
   extends Suite
-    with BasesUtil
-    with LocusUtil {
+    with BasesUtil {
 
   test("mappedread is mapped") {
-    val read = MappedRead(
-      "read1",
-      "TCGACCCTCGA",
-      Array[Byte]((10 to 20).map(_.toByte): _*),
-      isDuplicate = true,
-      "chr5",
-      50,
-      325352323,
-      TextCigarCodec.decode(""),
-      failedVendorQualityChecks = false,
-      isPositiveStrand = true,
-      isPaired = true
-    )
+    val read =
+      MappedRead(
+        "read1",
+        "TCGACCCTCGA",
+        Array[Byte]((10 to 20).map(_.toByte): _*),
+        isDuplicate = true,
+        "chr5",
+        50,
+        325352323,
+        TextCigarCodec.decode(""),
+        failedVendorQualityChecks = false,
+        isPositiveStrand = true,
+        isPaired = true
+      )
 
     read.isMapped should be(true)
     read.asInstanceOf[Read].isMapped should be(true)
   }
 
   test("mixed collections mapped and unmapped reads") {
-    val uread = UnmappedRead(
-      "read1",
-      "TCGACCCTCGA",
-      Array[Byte]((10 to 20).map(_.toByte): _*),
-      isDuplicate = true,
-      failedVendorQualityChecks = false,
-      isPaired = true
-    )
+    val uread =
+      UnmappedRead(
+        "read1",
+        "TCGACCCTCGA",
+        Array[Byte]((10 to 20).map(_.toByte): _*),
+        isDuplicate = true,
+        failedVendorQualityChecks = false,
+        isPaired = true
+      )
 
-    val mread = MappedRead(
-      "read1",
-      "TCGACCCTCGA",
-      Array[Byte]((10 to 20).map(_.toByte): _*),
-      isDuplicate = true,
-      "chr5",
-      50,
-      325352323,
-      TextCigarCodec.decode(""),
-      failedVendorQualityChecks = false,
-      isPositiveStrand = true,
-      isPaired = true
-    )
+    val mread =
+      MappedRead(
+        "read1",
+        "TCGACCCTCGA",
+        Array[Byte]((10 to 20).map(_.toByte): _*),
+        isDuplicate = true,
+        "chr5",
+        50,
+        325352323,
+        TextCigarCodec.decode(""),
+        failedVendorQualityChecks = false,
+        isPositiveStrand = true,
+        isPaired = true
+      )
 
     val collectionMappedReads: Seq[Read] = Seq(uread, mread)
     collectionMappedReads(0).isMapped should ===(false)

diff --git a/src/test/scala/org/hammerlab/genomics/reads/PairedReadSuite.scala b/src/test/scala/org/hammerlab/genomics/reads/PairedReadSuite.scala
@@ -2,13 +2,12 @@ package org.hammerlab.genomics.reads
 
 import htsjdk.samtools.TextCigarCodec
 import org.hammerlab.genomics.bases.BasesUtil
-import org.hammerlab.genomics.reference.test.LocusUtil
+import org.hammerlab.genomics.reference.test.LociConversions._
 import org.hammerlab.test.Suite
 
 class PairedReadSuite
   extends Suite
-    with BasesUtil
-    with LocusUtil {
+    with BasesUtil {
 
   test("unmappedread paired read is not mapped") {
     val unmappedRead =