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2 changes: 2 additions & 0 deletions
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...cts-identify/expected-cis-splice-effects-identify-default-stranded-annotatedjunctions.out
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chrom start end name score strand splice_site acceptors_skipped exons_skipped donors_skipped anchor known_donor known_acceptor known_junction genes transcripts variant_info | ||
22 93668 97252 JUNC00000001 5 - CT-AC 0 0 0 N 0 0 0 NA NA 22:94626-94627 |
35 changes: 35 additions & 0 deletions
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...ects-identify/expected-cis-splice-effects-identify-default-stranded-annotatedvariants.out
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##fileformat=VCFv4.1 | ||
##FILTER=<ID=PASS,Description="All filters passed"> | ||
##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag"> | ||
##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\""> | ||
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | ||
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> | ||
##FILTER=<ID=q10,Description="Quality below 10"> | ||
##FILTER=<ID=test,Description="Testing filter"> | ||
##contig=<ID=22,assembly=b37,length=51304566> | ||
##test=<ID=4,IE=5> | ||
##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta | ||
##readme=AAAAAA | ||
##readme=BBBBBB | ||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> | ||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | ||
##INFO=<ID=STR,Number=1,Type=String,Description="Test string type"> | ||
##INFO=<ID=genes,Number=1,Type=String,Description="The Variant falls in the splice region of these genes"> | ||
##INFO=<ID=transcripts,Number=1,Type=String,Description="The Variant falls in the splice region of these transcripts"> | ||
##INFO=<ID=distances,Number=1,Type=String,Description="Vector of Min(Distance from start/end of exon in the transcript.)"> | ||
##INFO=<ID=annotations,Number=1,Type=String,Description="Does the variant fall in exonic/intronic splicing related space in the transcript."> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B | ||
22 38192 . G T 19.2 PASS AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=splicing_exonic GT:GQ 0/1:215 0/1:225 | ||
22 94627 . G C 29.2 PASS AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1;annotations=splicing_intronic GT:GQ 0/1:215 0/1:225 | ||
22 97780 . G T 29.2 PASS AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=splicing_exonic GT:GQ 0/1:215 0/1:225 | ||
22 167675 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic GT:GQ 0/1:215 0/1:225 | ||
22 167677 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=0,0,0,0;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic GT:GQ 0/1:215 0/1:225 | ||
22 167679 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic GT:GQ 0/1:215 0/1:225 | ||
22 175311 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic GT:GQ 0/1:215 0/1:225 | ||
22 175501 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic GT:GQ 0/1:215 0/1:225 | ||
22 206991 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244;distances=0;annotations=splicing_exonic GT:GQ 0/1:215 0/1:225 | ||
22 206993 . G T 29.2 PASS AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244;distances=2;annotations=splicing_exonic GT:GQ 0/1:215 0/1:225 |
1 change: 1 addition & 0 deletions
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...lice-effects-identify/expected-cis-splice-effects-identify-default-stranded-junctions.out
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22 93614 97301 JUNC00000001 5 - 93614 97301 255,0,0 2 54,50 0,3637 |
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tests/integration-test/data/junctions-extract/expected-stranded-a.out
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1 22379140 22405017 JUNC00000001 236 - 22379140 22405017 255,0,0 2 95,96 0,25781 | ||
1 22379151 22405017 JUNC00000002 261 + 22379151 22405017 255,0,0 2 84,96 0,25770 | ||
1 22379167 22405020 JUNC00000003 245 ? 22379167 22405020 255,0,0 2 68,99 0,25754 | ||
1 22379198 22400683 JUNC00000004 17 + 22379198 22400683 255,0,0 2 37,97 0,21388 | ||
1 22379202 22400683 JUNC00000005 18 - 22379202 22400683 255,0,0 2 33,97 0,21384 | ||
1 22379210 22400675 JUNC00000006 6 ? 22379210 22400675 255,0,0 2 25,89 0,21376 | ||
1 22379367 22404979 JUNC00000007 1 - 22379367 22404979 255,0,0 2 42,58 0,25554 | ||
1 22380382 22404963 JUNC00000010 1 - 22380382 22404963 255,0,0 2 58,42 0,24539 | ||
1 22400613 22405020 JUNC00000011 94 - 22400613 22405020 255,0,0 2 99,99 0,4308 | ||
1 22400615 22405020 JUNC00000012 119 + 22400615 22405020 255,0,0 2 97,99 0,4306 | ||
1 22400616 22405019 JUNC00000013 27 ? 22400616 22405019 255,0,0 2 96,98 0,4305 | ||
1 22404977 22408287 JUNC00000016 315 ? 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404977 22408287 JUNC00000014 1767 + 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404977 22408287 JUNC00000015 1814 - 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404983 22413017 JUNC00000017 7 - 22404983 22413017 255,0,0 2 93,86 0,7948 | ||
1 22405013 22405292 JUNC00000018 3 - 22405013 22405292 255,0,0 2 63,94 0,185 | ||
1 22405022 22413024 JUNC00000019 5 + 22405022 22413024 255,0,0 2 54,93 0,7909 | ||
1 22405283 22408281 JUNC00000024 6 + 22405283 22408281 255,0,0 2 91,67 0,2931 | ||
1 22405301 22408241 JUNC00000025 1 ? 22405301 22408241 255,0,0 2 73,27 0,2913 | ||
1 22405322 22408287 JUNC00000026 5 - 22405322 22408287 255,0,0 2 52,73 0,2892 | ||
1 22408214 22413030 JUNC00000022 241 ? 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408214 22413030 JUNC00000021 2371 + 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408214 22413030 JUNC00000020 2266 - 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408221 22412968 JUNC00000027 1 - 22408221 22412968 255,0,0 2 62,37 0,4710 | ||
1 22412942 22413260 JUNC00000028 1894 + 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22412942 22413260 JUNC00000029 2028 - 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22412942 22413260 JUNC00000030 196 ? 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22413260 22416446 JUNC00000032 31 ? 22413260 22416446 255,0,0 2 99,11 0,3175 | ||
1 22413260 22418018 JUNC00000033 144 ? 22413260 22418018 255,0,0 2 99,98 0,4660 | ||
1 22413260 22418019 JUNC00000031 326 + 22413260 22418019 255,0,0 2 99,99 0,4660 | ||
1 22413261 22418019 JUNC00000034 450 - 22413261 22418019 255,0,0 2 98,99 0,4659 | ||
1 22413262 22416494 JUNC00000035 12 - 22413262 22416494 255,0,0 2 97,59 0,3173 | ||
1 22413274 22416494 JUNC00000036 15 + 22413274 22416494 255,0,0 2 85,59 0,3161 | ||
1 22413276 22481449 JUNC00000037 4 - 22413276 22481449 255,0,0 2 83,54 0,68119 | ||
1 22413278 22481419 JUNC00000038 4 + 22413278 22481419 255,0,0 2 81,24 0,68117 | ||
1 22413280 22418023 JUNC00000039 10 - 22413280 22418023 255,0,0 2 79,99 0,4644 | ||
1 22413282 22481418 JUNC00000040 1 ? 22413282 22481418 255,0,0 2 77,23 0,68113 | ||
1 22413287 22498575 JUNC00000041 1 + 22413287 22498575 255,0,0 2 72,28 0,85260 | ||
1 22413289 22418023 JUNC00000042 6 + 22413289 22418023 255,0,0 2 70,99 0,4635 | ||
1 22413295 22417924 JUNC00000043 2 + 22413295 22417924 255,0,0 2 64,36 0,4593 | ||
1 22413316 22456130 JUNC00000044 1 ? 22413316 22456130 255,0,0 2 43,55 0,42759 | ||
1 22413326 22498614 JUNC00000045 1 - 22413326 22498614 255,0,0 2 33,67 0,85221 | ||
1 22413335 22445230 JUNC00000046 1 + 22413335 22445230 255,0,0 2 24,76 0,31819 | ||
1 22446966 22447774 JUNC00000048 2 + 22446966 22447774 255,0,0 2 44,71 0,737 | ||
1 22446980 22447761 JUNC00000049 1 - 22446980 22447761 255,0,0 2 30,58 0,723 | ||
1 22447808 22448007 JUNC00000050 2 ? 22447808 22448007 255,0,0 2 38,70 0,129 | ||
1 22447816 22448007 JUNC00000051 1 + 22447816 22448007 255,0,0 2 30,70 0,121 | ||
1 22447997 22456136 JUNC00000052 1 + 22447997 22456136 255,0,0 2 72,28 0,8111 | ||
1 22469441 22481452 JUNC00000053 1 + 22469441 22481452 255,0,0 2 43,57 0,11954 |
41 changes: 41 additions & 0 deletions
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tests/integration-test/data/junctions-extract/expected-stranded-a30.out
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1 22379140 22405017 JUNC00000001 236 - 22379140 22405017 255,0,0 2 95,96 0,25781 | ||
1 22379151 22405017 JUNC00000002 261 + 22379151 22405017 255,0,0 2 84,96 0,25770 | ||
1 22379167 22405020 JUNC00000003 245 ? 22379167 22405020 255,0,0 2 68,99 0,25754 | ||
1 22379198 22400683 JUNC00000004 17 + 22379198 22400683 255,0,0 2 37,97 0,21388 | ||
1 22379202 22400683 JUNC00000005 18 - 22379202 22400683 255,0,0 2 33,97 0,21384 | ||
1 22379367 22404979 JUNC00000007 1 - 22379367 22404979 255,0,0 2 42,58 0,25554 | ||
1 22380382 22404963 JUNC00000010 1 - 22380382 22404963 255,0,0 2 58,42 0,24539 | ||
1 22400613 22405020 JUNC00000011 94 - 22400613 22405020 255,0,0 2 99,99 0,4308 | ||
1 22400615 22405020 JUNC00000012 119 + 22400615 22405020 255,0,0 2 97,99 0,4306 | ||
1 22400616 22405019 JUNC00000013 27 ? 22400616 22405019 255,0,0 2 96,98 0,4305 | ||
1 22404977 22408287 JUNC00000016 315 ? 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404977 22408287 JUNC00000014 1767 + 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404977 22408287 JUNC00000015 1814 - 22404977 22408287 255,0,0 2 99,73 0,3237 | ||
1 22404983 22413017 JUNC00000017 7 - 22404983 22413017 255,0,0 2 93,86 0,7948 | ||
1 22405013 22405292 JUNC00000018 3 - 22405013 22405292 255,0,0 2 63,94 0,185 | ||
1 22405022 22413024 JUNC00000019 5 + 22405022 22413024 255,0,0 2 54,93 0,7909 | ||
1 22405283 22408281 JUNC00000024 6 + 22405283 22408281 255,0,0 2 91,67 0,2931 | ||
1 22405322 22408287 JUNC00000026 5 - 22405322 22408287 255,0,0 2 52,73 0,2892 | ||
1 22408214 22413030 JUNC00000022 241 ? 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408214 22413030 JUNC00000021 2371 + 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408214 22413030 JUNC00000020 2266 - 22408214 22413030 255,0,0 2 73,99 0,4717 | ||
1 22408221 22412968 JUNC00000027 1 - 22408221 22412968 255,0,0 2 62,37 0,4710 | ||
1 22412942 22413260 JUNC00000028 1894 + 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22412942 22413260 JUNC00000029 2028 - 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22412942 22413260 JUNC00000030 196 ? 22412942 22413260 255,0,0 2 99,99 0,219 | ||
1 22413260 22418018 JUNC00000033 144 ? 22413260 22418018 255,0,0 2 99,98 0,4660 | ||
1 22413260 22418019 JUNC00000031 326 + 22413260 22418019 255,0,0 2 99,99 0,4660 | ||
1 22413261 22418019 JUNC00000034 450 - 22413261 22418019 255,0,0 2 98,99 0,4659 | ||
1 22413262 22416494 JUNC00000035 12 - 22413262 22416494 255,0,0 2 97,59 0,3173 | ||
1 22413274 22416494 JUNC00000036 15 + 22413274 22416494 255,0,0 2 85,59 0,3161 | ||
1 22413276 22481449 JUNC00000037 4 - 22413276 22481449 255,0,0 2 83,54 0,68119 | ||
1 22413280 22418023 JUNC00000039 10 - 22413280 22418023 255,0,0 2 79,99 0,4644 | ||
1 22413289 22418023 JUNC00000042 6 + 22413289 22418023 255,0,0 2 70,99 0,4635 | ||
1 22413295 22417924 JUNC00000043 2 + 22413295 22417924 255,0,0 2 64,36 0,4593 | ||
1 22413316 22456130 JUNC00000044 1 ? 22413316 22456130 255,0,0 2 43,55 0,42759 | ||
1 22413326 22498614 JUNC00000045 1 - 22413326 22498614 255,0,0 2 33,67 0,85221 | ||
1 22446966 22447774 JUNC00000048 2 + 22446966 22447774 255,0,0 2 44,71 0,737 | ||
1 22446980 22447761 JUNC00000049 1 - 22446980 22447761 255,0,0 2 30,58 0,723 | ||
1 22447808 22448007 JUNC00000050 2 ? 22447808 22448007 255,0,0 2 38,70 0,129 | ||
1 22447816 22448007 JUNC00000051 1 + 22447816 22448007 255,0,0 2 30,70 0,121 | ||
1 22469441 22481452 JUNC00000053 1 + 22469441 22481452 255,0,0 2 43,57 0,11954 |
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