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114
src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala
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| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.models | ||
|
|
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| import org.bdgenomics.adam.util.ADAMFunSuite | ||
| import org.bdgenomics.formats.avro.Feature | ||
|
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| class CoverageSuite | ||
| extends ADAMFunSuite { | ||
|
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| test("Convert to coverage from valid Feature") { | ||
| // create a valid feature | ||
| val featureToConvert = | ||
| Feature.newBuilder() | ||
| .setContigName("chr1") | ||
| .setStart(1) | ||
| .setEnd(2) | ||
| .setScore(100) | ||
| .build() | ||
|
|
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| val coverageAfterConversion = Coverage(featureToConvert) | ||
|
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| // all fields should match between the two | ||
| assert(coverageAfterConversion.start == featureToConvert.start) | ||
| assert(coverageAfterConversion.end == featureToConvert.end) | ||
| assert(coverageAfterConversion.contigName === featureToConvert.getContigName) | ||
| assert(coverageAfterConversion.count == featureToConvert.score) | ||
| } | ||
|
|
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| test("Convert to coverage from Feature with null/empty contigName fails with correct error") { | ||
| // feature with empty contigname is not valid when converting to Coverage | ||
| val featureWithEmptyContigName = | ||
| Feature.newBuilder() | ||
| .setContigName("") | ||
| .setStart(1) | ||
| .setEnd(2) | ||
| .setScore(100) | ||
| .build() | ||
|
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| val caughtWithEmptyContigName = | ||
| intercept[IllegalArgumentException](Coverage(featureWithEmptyContigName)) | ||
|
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| assert(caughtWithEmptyContigName.getMessage == "requirement failed: Features must have Contig name to convert to Coverage") | ||
| // feature without contigname is not valid when converting to Coverage | ||
| val featureWithNullContigName = | ||
| Feature.newBuilder() | ||
| .setStart(1) | ||
| .setEnd(2) | ||
| .setScore(100) | ||
| .build() | ||
|
|
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| val caughtWithNullContigName = | ||
| intercept[IllegalArgumentException](Coverage(featureWithNullContigName)) | ||
|
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| assert(caughtWithNullContigName.getMessage == "requirement failed: Features must have Contig name to convert to Coverage") | ||
| } | ||
|
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| test("Convert to coverage from Feature with no start/end position fails with correct error") { | ||
| // feature without start position is invalid when converting to Coverage | ||
| val featureWithoutStartPosition = | ||
| Feature.newBuilder() | ||
| .setContigName("chr1") | ||
| .setEnd(2) | ||
| .setScore(100) | ||
| .build() | ||
|
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| val caughtWithoutStartPosition = | ||
| intercept[IllegalArgumentException](Coverage(featureWithoutStartPosition)) | ||
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| assert(caughtWithoutStartPosition.getMessage == "requirement failed: Features must have valid position data to convert to Coverage") | ||
| // feature without end position is invalid when converting to Coverage | ||
| val featureWithoutEndPosition = | ||
| Feature.newBuilder() | ||
| .setContigName("chr1") | ||
| .setStart(1) | ||
| .setScore(100) | ||
| .build() | ||
|
|
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| val caughtWithoutEndPosition = | ||
| intercept[IllegalArgumentException](Coverage(featureWithoutEndPosition)) | ||
|
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| assert(caughtWithoutEndPosition.getMessage == "requirement failed: Features must have valid position data to convert to Coverage") | ||
| } | ||
|
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| test("Convert to coverage from Feature with no score fails with correct error") { | ||
| // feature without score is invalid when converting to Coverage | ||
| val featureWithoutScore = | ||
| Feature.newBuilder() | ||
| .setContigName("chr1") | ||
| .setStart(1) | ||
| .setEnd(2) | ||
| .build() | ||
|
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| val caughtWithoutScore = | ||
| intercept[IllegalArgumentException](Coverage(featureWithoutScore)) | ||
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| assert(caughtWithoutScore.getMessage == "requirement failed: Features must have valid score to convert to Coverage") | ||
| } | ||
| } |