Package org.snpeff.snpEffect.testCases.unity

Class Summary

Class	Description
TestCasesAlign	test cases for Sequence alignment
TestCasesAnnParse	Test case for parsing ANN fields
TestCasesApplyDel	Test cases: apply a variant (DEL) to a transcript
TestCasesApplyIns	Test cases: apply a variant (INS) to a transcript
TestCasesApplyMixed	Test cases: apply a variant (MIXED) to a transcript
TestCasesApplyMnp	Test cases: apply a variant (MNP) to a transcript
TestCasesApplySnp	Test cases: apply a variant (SNP) to a transcript
TestCasesBase	Base class for some test cases
TestCasesBaseApply	Test case Transcript: 1:0-999, strand: +, id:transcript1, Protein Exons: 1:100-199 'exon1', rank: 1, frame: ., sequence: atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg 1:300-399 'exon2', rank: 2, frame: ., sequence: tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg 1:900-999 'exon3', rank: 0, frame: ., sequence: ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg CDS : atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatggtgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacgggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg Protein : MSAGEGIHAARILMLPRWILSEIWCPGREGHIMVFGNSRARFCSKLNWQLGINPDPIVTHGSIHPQRVEEKHLTPIEQDLFRNTLYRLPIYLIPHIYFIG Transcript (full coordinates): 0 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 ....................................................................................................atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg....................................................................................................tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg M S A G E G I H A A R I L M L P R W I L S E I W C P G R E G H I M V F G N S R A R F C S K L N W Q L G I N P D P I V T H G S I H P Q R V E E K H L T P I E Q D L F R N T L Y R L P I Y L I P H I Y F I G 0120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120 1201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201 2012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012 ---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | | | | | | | | | | | |^999 | | | | |^900 | | | |^399 | | |^300 | |^199 |^100
TestCasesBinomial	Test for Binomial distribution
TestCasesBuild	Test case
TestCasesCds	Test random SNP changes
TestCasesChiSquare	Test for Hypergeometric distribution and Fisher exact test
TestCasesCircular	Test cases for circular genomes
TestCasesCochranArmitage	Cochran-Armitage test statistic test case
TestCasesCodonTable	Codon tables
TestCasesCytoBands	Test case for cytobands
TestCasesDel	Test random DEL changes
TestCasesDels	Test random DEL changes
TestCasesDnaNSequence
TestCasesDnaOverlap
TestCasesDnaSequence
TestCasesDnaSequenceByte
TestCasesEffectCollapse	Test Splice sites variants The sample transcript used is: Transcript:1:751-1139, strand: +, id:transcript_0, Protein Exons: 1:751-810 'exon_0_0', rank: 1, frame: ., sequence: cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgca 1:1013-1139 'exon_0_1', rank: 2, frame: ., sequence: cttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa CDS : cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgcacttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa Protein : RLTYIVMSFVGP*DFAQNRALRLLGGLSTFSAGKVIYACAQPW*QGFTAPLMV*PKPHTSHP?
TestCasesEffectCollapse2	Test case
TestCasesFasta	Test case for FASTA file parsing
TestCasesFileIndexChrPos	Test cases for file index (chr:pos index on files)
TestCasesFisherExactTest	Test for Hypergeometric distribution and Fisher exact test
TestCasesGenePvalueList	GenePvalueList statistics test case
TestCasesGenomicSequences	Test case
TestCasesGenotypeVector	Test cases for GenotypeVector class
TestCasesHgvs	Test case for basic HGV annotaions
TestCasesHgvsDnaDup	Test case
TestCasesHgvsDnaDupNegative	Test cases for HGVS's 'dup' on the negative strand
TestCasesHgvsProtDup	Test case
TestCasesHypergeometric	Test for Hypergeometric distribution and Fisher exact test
TestCasesIns	Test random SNP changes
TestCasesIntergenic	Test intergenic markers
TestCasesIntervals
TestCasesIntervalTree	Test case for interval tree structure
TestCasesIntervalTreeArray	Test case for interval tree structure
TestCasesIntervalTreeOri	Test case for interval tree structure
TestCasesIntervalVariant	Test random Interval Variants (e.g.
TestCasesIntStats
TestCasesIubString
TestCasesJaspar	Test case for Jaspar parsing
TestCasesMarkerUtils
TestCasesMnps	Test random SNP changes
TestCasesNmers
TestCasesOverlap
TestCasesProteinInteraction	Test cases for protein interaction
TestCasesReactome	Test Reactome circuits
TestCasesSeekableReader	Seekable file reader test case
TestCasesSequenceIndexer
TestCasesSnps	Test random SNP changes
TestCasesSpliceRegion	Test Splice sites variants
TestCasesSpliceSite	Test Splice sites variants
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? 1 0 1 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567 gttgcttgaatactgtatagccttgccattgt........................................................tgtgttgctaact..........................................................................................agacatggac V A * I L Y S L A I V V L L T R H G 01201201201201201201201201201201 2012012012012 0120120120 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------->>>>>>>>>>>>>------------------------------------------------------------------------------------------>>>>>>>>>> | | | | | | | | | | | ^1157 | | | | ^1148 | | | ^1057 | | ^1045 | ^988 ^957 Gene: geneId2 1:2066-2141, strand: +, id:transcript_1, Protein Exons: 1:2066-2069 'exon_1_0', rank: 1, frame: ., sequence: actt 1:2084-2089 'exon_1_1', rank: 2, frame: ., sequence: cccttt 1:2116-2126 'exon_1_2', rank: 3, frame: ., sequence: tacgcccacgt 1:2133-2141 'exon_1_3', rank: 4, frame: ., sequence: ccgccgctg CDS : acttcccttttacgcccacgtccgccgctg Protein : TSLLRPRPPL 1 7 8 9 0 1 2 3 4 6789012345678901234567890123456789012345678901234567890123456789012345678901 actt..............cccttt..........................tacgcccacgt......ccgccgctg T S L L R P R P P L 0120 120120 12012012012 012012012 >>>>-------------->>>>>>-------------------------->>>>>>>>>>>------>>>>>>>>> | | | | | | | | | | | | | | | ^2141 | | | | | | ^2133 | | | | | ^2126 | | | | ^2116 | | | ^2089 | | ^2084 | ^2069 ^2066
TestCasesStructuralDup	Test case for structural variants: Duplications
TestCasesStructuralInv	Test cases for structural variants: Inversions Gene models used in these test cases: Gene: Gene_1:953-1216 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? 1 0 1 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567 gttgcttgaatactgtatagccttgccattgt........................................................tgtgttgctaact..........................................................................................agacatggac V A * I L Y S L A I V V L L T R H G 01201201201201201201201201201201 2012012012012 0120120120 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------->>>>>>>>>>>>>------------------------------------------------------------------------------------------>>>>>>>>>> | | | | | | | | | | | ^1157 | | | | ^1148 | | | ^1057 | | ^1045 | ^988 ^957 Gene: Gene_1:2057-2157 1:2066-2141, strand: +, id:transcript_1, Protein Exons: 1:2066-2069 'exon_1_0', rank: 1, frame: ., sequence: actt 1:2084-2089 'exon_1_1', rank: 2, frame: ., sequence: cccttt 1:2116-2126 'exon_1_2', rank: 3, frame: ., sequence: tacgcccacgt 1:2133-2141 'exon_1_3', rank: 4, frame: ., sequence: ccgccgctg CDS : acttcccttttacgcccacgtccgccgctg Protein : TSLLRPRPPL 1 7 8 9 0 1 2 3 4 6789012345678901234567890123456789012345678901234567890123456789012345678901 actt..............cccttt..........................tacgcccacgt......ccgccgctg T S L L R P R P P L 0120 120120 12012012012 012012012 >>>>-------------->>>>>>-------------------------->>>>>>>>>>>------>>>>>>>>> | | | | | | | | | | | | | | | ^2141 | | | | | | ^2133 | | | | | ^2126 | | | | ^2116 | | | ^2089 | | ^2084 | ^2069 ^2066
TestCasesStructuralTranslocations	Test case for structural variants: Translocation (fusions) We create two genes (one transcript each).
TestCasesVariantDecompose	Test cases: apply a variant (MIXED) to a transcript
TestCasesVariantRealignment	Test cases for variant realignment
TestCasesVcf	VCF parsing test cases
TestCasesZzz	Test random SNP changes