TestCasesAlign |
test cases for Sequence alignment
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TestCasesAnnParse |
Test case for parsing ANN fields
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TestCasesApplyDel |
Test cases: apply a variant (DEL) to a transcript
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TestCasesApplyIns |
Test cases: apply a variant (INS) to a transcript
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TestCasesApplyMixed |
Test cases: apply a variant (MIXED) to a transcript
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TestCasesApplyMnp |
Test cases: apply a variant (MNP) to a transcript
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TestCasesApplySnp |
Test cases: apply a variant (SNP) to a transcript
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TestCasesBase |
Base class for some test cases
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TestCasesBaseApply |
Test case
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TestCasesBinomial |
Test for Binomial distribution
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TestCasesBuild |
Test case
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TestCasesCds |
Test random SNP changes
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TestCasesChiSquare |
Test for Hypergeometric distribution and Fisher exact test
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TestCasesCircular |
Test cases for circular genomes
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TestCasesCochranArmitage |
Cochran-Armitage test statistic test case
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TestCasesCodonTable |
Codon tables
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TestCasesCytoBands |
Test case for cytobands
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TestCasesDel |
Test random DEL changes
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TestCasesDels |
Test random DEL changes
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TestCasesDnaNSequence |
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TestCasesDnaOverlap |
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TestCasesDnaSequence |
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TestCasesDnaSequenceByte |
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TestCasesEffectCollapse |
Test Splice sites variants
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TestCasesEffectCollapse2 |
Test case
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TestCasesFasta |
Test case for FASTA file parsing
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TestCasesFileIndexChrPos |
Test cases for file index (chr:pos index on files)
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TestCasesFisherExactTest |
Test for Hypergeometric distribution and Fisher exact test
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TestCasesGenePvalueList |
GenePvalueList statistics test case
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TestCasesGenomicSequences |
Test case
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TestCasesGenotypeVector |
Test cases for GenotypeVector class
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TestCasesHgvs |
Test case for basic HGV annotations
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TestCasesHgvsDnaDup |
Test case
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TestCasesHgvsDnaDupNegative |
Test cases for HGVS's 'dup' on the negative strand
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TestCasesHgvsExon |
Test random SNP changes
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TestCasesHgvsIntron |
Test random SNP changes
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TestCasesHgvsProtDup |
Test case
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TestCasesHypergeometric |
Test for Hypergeometric distribution and Fisher exact test
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TestCasesIns |
Test random SNP changes
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TestCasesIntergenic |
Test intergenic markers
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TestCasesIntervals |
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TestCasesIntervalTree |
Test case for interval tree structure
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TestCasesIntervalTreeArray |
Test case for interval tree structure
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TestCasesIntervalTreeOri |
Test case for interval tree structure
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TestCasesIntervalVariant |
Test random Interval Variants (e.g.
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TestCasesIntStats |
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TestCasesIubString |
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TestCasesJaspar |
Test case for Jaspar parsing
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TestCasesMarkerUtils |
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TestCasesMnps |
Test random SNP changes
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TestCasesNextProt |
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TestCasesNmers |
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TestCasesOverlap |
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TestCasesProteinInteraction |
Test cases for protein interaction
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TestCasesReactome |
Test Reactome circuits
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TestCasesSeekableReader |
Seekable file reader test case
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TestCasesSequenceIndexer |
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TestCasesSnps |
Test random SNP changes
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TestCasesSpliceRegion |
Test Splice sites variants
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TestCasesSpliceSite |
Test Splice sites variants
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TestCasesStructuralDel |
Test case
Gene: geneId1
1:957-1157, strand: +, id:transcript_0, Protein
Exons:
1:957-988 'exon_0_0', rank: 1, frame: ., sequence: gttgcttgaatactgtatagccttgccattgt
1:1045-1057 'exon_0_1', rank: 2, frame: ., sequence: tgtgttgctaact
1:1148-1157 'exon_0_2', rank: 3, frame: ., sequence: agacatggac
CDS : gttgcttgaatactgtatagccttgccattgttgtgttgctaactagacatggac
Protein : VA*ILYSLAIVVLLTRHG?
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TestCasesStructuralDup |
Test case for structural variants: Duplications
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TestCasesStructuralInv |
Test cases for structural variants: Inversions
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TestCasesStructuralTranslocations |
Test case for structural variants: Translocation (fusions)
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TestCasesVariantDecompose |
Test cases: apply a variant (MIXED) to a transcript
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TestCasesVariantRealignment |
Test cases for variant realignment
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TestCasesVcf |
VCF parsing test cases
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TestCasesZzz |
Test playground
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TestGenome |
Creates a simple "genome" for testing:
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