Class TestCasesDnaSequence
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
-
Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
randDnaSeqGetBasesTest
(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence.void
randDnaSeqGetBaseTest
(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence.void
randDnaSeqTest
(int numTests, int lenMask, long seed) Create random sequences and compare to storing them in a DnaSequencevoid
randReplaceBaseTest
(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence.void
randTestQual
(int numTests, int lenMask, long seed) Create random sequences (and qualities) and compare to storing them in a DnaAndQualityvoid
void
void
void
void
void
void
void
void
void
void
void
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
-
Constructor Details
-
TestCasesDnaSequence
public TestCasesDnaSequence()
-
-
Method Details
-
randDnaSeqGetBasesTest
public void randDnaSeqGetBasesTest(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence. Compare getting a few random bases from the original and DnaSequence sequences. -
randDnaSeqGetBaseTest
public void randDnaSeqGetBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence. Compare getting a single random base from the original and DnaSequence sequences. -
randDnaSeqTest
public void randDnaSeqTest(int numTests, int lenMask, long seed) Create random sequences and compare to storing them in a DnaSequence -
randReplaceBaseTest
public void randReplaceBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed) Create random sequences and store them in a DnaSequence. Compare after replacing random bases from the original and DnaSequence sequences. -
randTestQual
public void randTestQual(int numTests, int lenMask, long seed) Create random sequences (and qualities) and compare to storing them in a DnaAndQuality -
test_01_short
@Test public void test_01_short() -
test_01_short_getBase
@Test public void test_01_short_getBase() -
test_01_short_getBases
@Test public void test_01_short_getBases() -
test_01_short_replaceBase
@Test public void test_01_short_replaceBase() -
test_02_long
@Test public void test_02_long() -
test_02_long_getBase
@Test public void test_02_long_getBase() -
test_02_long_getBases
@Test public void test_02_long_getBases() -
test_02_long_replaceBase
@Test public void test_02_long_replaceBase() -
test_04_Pe
@Test public void test_04_Pe() -
test_05_fastqReader
@Test public void test_05_fastqReader() -
test_05_quality_short
@Test public void test_05_quality_short() -
test_06_quality_long
@Test public void test_06_quality_long()
-