From 07d3c1ab338f2c850bcbcfdb15debf3b6a02bede Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Thu, 20 Sep 2018 13:49:57 -0500 Subject: [PATCH] Clean up fields and doc in fragment. --- .../adam/converters/FastqRecordConverter.scala | 2 +- .../bdgenomics/adam/rdd/read/SingleReadBucket.scala | 6 +++--- .../converters/AlignmentRecordConverterSuite.scala | 4 ++-- .../adam/converters/FastqRecordConverterSuite.scala | 4 ++-- .../rdd/contig/NucleotideContigFragmentRDDSuite.scala | 2 +- .../bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala | 2 +- .../bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala | 2 +- .../adam/rdd/read/AlignmentRecordRDDSuite.scala | 2 +- .../bdgenomics/adam/rdd/read/BinQualitiesSuite.scala | 4 ++-- .../adam/rdd/read/SingleReadBucketSuite.scala | 10 +++++----- .../bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala | 2 +- .../bdgenomics/adam/rdd/variant/VariantRDDSuite.scala | 2 +- pom.xml | 2 +- 13 files changed, 22 insertions(+), 22 deletions(-) diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala index a9af97fc0b..6535d5b65f 100644 --- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala +++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala @@ -253,7 +253,7 @@ private[adam] class FastqRecordConverter extends Serializable with Logging { // build and return record Fragment.newBuilder - .setReadName(firstReadName) + .setName(firstReadName) .setAlignments(alignments) .build } diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala index a0d3f492b3..4eaaf7791b 100644 --- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala +++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala @@ -142,20 +142,20 @@ private[adam] case class SingleReadBucket( // start building fragment val builder = Fragment.newBuilder() - .setReadName(unionReads.head.getReadName) + .setName(unionReads.head.getReadName) .setAlignments(seqAsJavaList(allReads.toSeq)) // is an insert size defined for this fragment? primaryMapped.headOption .foreach(r => { Option(r.getInferredInsertSize).foreach(is => { - builder.setFragmentSize(is.toInt) + builder.setInsertSize(is.toInt) }) }) // set record group name, if known Option(unionReads.head.getRecordGroupName) - .foreach(n => builder.setRunId(n)) + .foreach(n => builder.setRecordGroupName(n)) builder.build() } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala index d209d52de9..45167cc9b3 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala @@ -270,7 +270,7 @@ class AlignmentRecordConverterSuite extends FunSuite { .build()) val fragment = Fragment.newBuilder() - .setReadName("testRead") + .setName("testRead") .setAlignments(seqAsJavaList(alignments)) .build() @@ -307,7 +307,7 @@ class AlignmentRecordConverterSuite extends FunSuite { .setQual("?????*****") .build()) val fragment = Fragment.newBuilder() - .setReadName("testRead") + .setName("testRead") .setAlignments(seqAsJavaList(alignments)) .build() diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala index 17c3215d2a..71f438c8f7 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala @@ -130,7 +130,7 @@ class FastqRecordConverterSuite extends FunSuite with PrivateMethodTester { test("testing FastqRecordConverter.convertFragment with valid input") { val input = (null, new Text("@read\nATCGA\n+\nabcde\n@read\nTCGAT\n+\n12345")) val fragment = converter.convertFragment(input) - assert(fragment.getReadName == "read") + assert(fragment.getName == "read") // more detailed testing val align1 = fragment.getAlignments.get(0) @@ -151,7 +151,7 @@ class FastqRecordConverterSuite extends FunSuite with PrivateMethodTester { test("testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes") { val input = (null, new Text("@read/1\nATCGA\n+\nabcde\n@read/2\nTCGAT\n+\n12345")) val fragment = converter.convertFragment(input) - assert(fragment.getReadName == "read") + assert(fragment.getName == "read") // more detailed testing val align1 = fragment.getAlignments.get(0) diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala index 393a07e000..3b1042050f 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala @@ -64,7 +64,7 @@ object NucleotideContigFragmentRDDSuite extends Serializable { def fragFn(ncf: NucleotideContigFragment): Fragment = { Fragment.newBuilder - .setReadName(ncf.getContigName) + .setName(ncf.getContigName) .build } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala index 0cb5fb1fb1..8d08b54c25 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala @@ -67,7 +67,7 @@ object CoverageRDDSuite extends Serializable { def fragFn(cov: Coverage): Fragment = { Fragment.newBuilder - .setReadName(cov.contigName) + .setName(cov.contigName) .build } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala index aca8b9b148..1254c9467f 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala @@ -59,7 +59,7 @@ object FeatureRDDSuite extends Serializable { def fragFn(f: Feature): Fragment = { Fragment.newBuilder - .setReadName(f.getContigName) + .setName(f.getContigName) .build } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala index 65504d96db..de12c5b743 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala @@ -123,7 +123,7 @@ object AlignmentRecordRDDSuite extends Serializable { def fragFn(r: AlignmentRecord): Fragment = { Fragment.newBuilder - .setReadName(r.getReadName) + .setName(r.getReadName) .build } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala index 171ed08d89..e82e10df71 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala @@ -177,14 +177,14 @@ class BinQualitiesSuite extends ADAMFunSuite { testQuals(newRead.getQual) val fragment = Fragment.newBuilder - .setReadName("testFragment") + .setName("testFragment") .setAlignments(List(read)) .build val newFragment = BinQualities.binFragment(fragment, bins) assert(newFragment.getAlignments.size === 1) - assert(newFragment.getReadName === "testFragment") + assert(newFragment.getName === "testFragment") testQuals(newFragment.getAlignments.head.getQual) } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala index f1eeeb4c1f..cff53ac1f0 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala @@ -39,7 +39,7 @@ class SingleReadBucketSuite extends FunSuite { val srb = SingleReadBucket(unmapped = reads) val fragment = srb.toFragment assert(fragment.getAlignments.size === 2) - assert(fragment.getReadName === "myRead") + assert(fragment.getName === "myRead") } test("convert proper pair to fragment") { @@ -74,8 +74,8 @@ class SingleReadBucketSuite extends FunSuite { .build()) val srb = SingleReadBucket(primaryMapped = reads) val fragment = srb.toFragment - assert(fragment.getFragmentSize === 8) - assert(fragment.getReadName === "myRead") + assert(fragment.getInsertSize === 8) + assert(fragment.getName === "myRead") assert(fragment.getAlignments.size === 2) } @@ -125,8 +125,8 @@ class SingleReadBucketSuite extends FunSuite { .build()) val srb = SingleReadBucket(primaryMapped = reads, secondaryMapped = chimera) val fragment = srb.toFragment - assert(fragment.getFragmentSize === null) - assert(fragment.getReadName === "myRead") + assert(fragment.getInsertSize === null) + assert(fragment.getName === "myRead") assert(fragment.getAlignments.size === 3) } } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala index 1a8c028049..83bb34d6c7 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala @@ -66,7 +66,7 @@ object GenotypeRDDSuite extends Serializable { def fragFn(g: Genotype): Fragment = { Fragment.newBuilder - .setReadName(g.getContigName) + .setName(g.getContigName) .build } diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala index 6f640d6122..001f59ed5c 100644 --- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala +++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala @@ -70,7 +70,7 @@ object VariantRDDSuite extends Serializable { def fragFn(v: Variant): Fragment = { Fragment.newBuilder - .setReadName(v.getContigName) + .setName(v.getContigName) .build } diff --git a/pom.xml b/pom.xml index f61b878dd7..a5e768e5c7 100644 --- a/pom.xml +++ b/pom.xml @@ -27,7 +27,7 @@ 2.7.3 7.9.2 1.7.25 - 0.11.3 + 0.12.0-SNAPSHOT 0.2.13 2.13.2 1.1.1