Merge pull request #363 from hammerlab/adam018-upgrade

Upgrade to ADAM 0.18

pom.xml

@@ -16,8 +16,8 @@
   <name>guacamole: variant caller</name>
 
   <properties>
-    <adam.version>0.17.0</adam.version>
-    <bdg-formats.version>0.4.0</bdg-formats.version>
+    <adam.version>0.18.1</adam.version>
+    <bdg-formats.version>0.6.1</bdg-formats.version>
     <java.version>1.8</java.version>
     <scala.version>2.10.3</scala.version>
     <scala.version.prefix>2.10</scala.version.prefix>

src/main/scala/org/hammerlab/guacamole/reads/MappedRead.scala

@@ -126,7 +126,7 @@ object MappedRead {
     isPaired: Boolean)(implicit d: DummyImplicit): MappedRead = MappedRead(
     token, sequence, baseQualities, isDuplicate, sampleName, referenceContig,
     alignmentQuality, start, cigar,
-    mdTagString.map(MdTag(_, start)),
+    mdTagString.map(MdTag(_, start, cigar)),
     failedVendorQualityChecks, isPositiveStrand, isPaired)
 }
 

src/main/scala/org/hammerlab/guacamole/reads/Read.scala

@@ -446,7 +446,7 @@ object Read extends Logging {
       )
       else
         None
-      PairedRead(read, isFirstInPair = alignmentRecord.getFirstOfPair, mateAlignment)
+      PairedRead(read, isFirstInPair = alignmentRecord.getReadNum == 1, mateAlignment)
     } else {
       read
     }

src/test/resources/different_start_reads.sam

@@ -1,10 +1,9 @@
 @HD	VN:1.3	SO:coordinate
 @SQ	SN:artificial	LN:1120
 read1	67	artificial	6	90	29M10D31M	=	1	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:20	MD:Z:29^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G11
-read2	67	artificial	11	90	5M5I34M10D16M	=	1	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:30	MD:Z:24G0G0G0G0G0G0G0G0G0G10^GGGGGGGGGG0A0A0A0A0A0A0A0A0A0A6
+read2	67	artificial	11	90	5M5I39M10D16M	=	1	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:30	MD:Z:24G0G0G0G0G0G0G0G0G0G10^GGGGGGGGGG0A0A0A0A0A0A0A0A0A0A6
 read3	67	artificial	16	90	19M10D41M	=	1	0	ATCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:20	MD:Z:19^GGGGGGGGGG10G0G0G0G0G0G0G0G0G0G21
 read4	67	artificial	21	90	10M10I10D40M	=	1	0	ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:30	MD:Z:10^GGGGGGGGGG40
 read5	67	artificial	11	90	5M4=1X5=	=	1	0	ACGTACGTACGTACG	IIIIIIIIIIIIIII	AS:i:70	XS:i:70	NM:i:20	MD:Z:9G5
 read6	131	artificial	41	90	4=1D4=4S	=	1	0	ACGTACGTACGT	IIIIIIIIIIII	MD:Z:4^G4
 read7	131	artificial	41	90	4=1D4=4H	=	1	0	ACGTACGT	IIIIIIII	MD:Z:4^G4
-read8	131	artificial	41	90	4=1P4=	=	1	0	ACGTACGT	IIIIIIII	MD:Z:8

src/test/scala/org/hammerlab/guacamole/pileup/PileupSuite.scala

@@ -18,12 +18,11 @@
 
 package org.hammerlab.guacamole.pileup
 
-import org.hammerlab.guacamole.commands.SomaticStandard
-import org.hammerlab.guacamole.util.{ TestUtil, GuacFunSuite }
-import TestUtil.Implicits._
-import TestUtil.assertBases
-import org.hammerlab.guacamole.reads.MappedRead
 import org.hammerlab.guacamole.Bases
+import org.hammerlab.guacamole.reads.MappedRead
+import org.hammerlab.guacamole.util.TestUtil.Implicits._
+import org.hammerlab.guacamole.util.TestUtil.assertBases
+import org.hammerlab.guacamole.util.{ GuacFunSuite, TestUtil }
 import org.hammerlab.guacamole.variants.Allele
 import org.scalatest.Matchers
 import org.scalatest.prop.TableDrivenPropertyChecks
@@ -378,28 +377,6 @@ class PileupSuite extends GuacFunSuite with Matchers with TableDrivenPropertyChe
     }
   }
 
-  sparkTest("Read8: ACGTACGT 4=1P4=") {
-
-    // Read8: ACGTACGT 4=1P4=
-    // one `P`, a silent deletion (i.e. a deletion from a reference with a
-    // virtual insertion)
-    // 4=1P4= should be equivalent to 8=
-    val decadentRead8 = testAdamRecords(7)
-    val read8At40 = pileupElementFromRead(decadentRead8, 40)
-    assert(read8At40 != null)
-    assertBases(advancePileupElement(read8At40, 40).sequencedBases, "A")
-    assertBases(advancePileupElement(read8At40, 41).sequencedBases, "C")
-    assertBases(advancePileupElement(read8At40, 42).sequencedBases, "G")
-    assertBases(advancePileupElement(read8At40, 43).sequencedBases, "T")
-    assertBases(advancePileupElement(read8At40, 44).sequencedBases, "A")
-    assertBases(advancePileupElement(read8At40, 45).sequencedBases, "C")
-    assertBases(advancePileupElement(read8At40, 46).sequencedBases, "G")
-    assertBases(advancePileupElement(read8At40, 47).sequencedBases, "T")
-    intercept[RuntimeException] {
-      advancePileupElement(read8At40, 48).sequencedBases
-    }
-  }
-
   test("create and advance pileup element from RNA read") {
     val rnaRead = TestUtil.makeRead(
       sequence = "CCCCAGCCTAGGCCTTCGACACTGGGGGGCTGAGGGAAGGGGCACCTGCC",

src/test/scala/org/hammerlab/guacamole/reads/MDTagUtilsSuite.scala

@@ -226,7 +226,9 @@ class MDTagUtilsSuite extends FunSuite with Matchers {
     reference.size should be(referenceLength)
     Bases.basesToString(reference.slice(0, 7).toSeq) should be("CCCCAGC")
     (Bases.basesToString(reference.slice(referenceLength - 43, referenceLength).toSeq)
-      should be("CTAGGCCTTCGACACTGGGGGGCTGAGGGAAGGGGCACCTGCC"))
+      // seq: CT[A]GGCCTTCGACACTGGGGGGCTGAG[G]GAAGGGG[C]ACCTGCC
+      // ref: CT[T]GGCCTTCGACACTGGGGGGCTGAG[T]GAAGGGG[G]ACCTGCC
+      should be("CTTGGCCTTCGACACTGGGGGGCTGAGTGAAGGGGGACCTGCC"))
 
   }