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yang-yangfengyang-yangfeng
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update test files to reflect the correct output, updated in fix_skip_counts, but also include gene ids
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‎tests/integration-test/data/cis-splice-effects-identify/expected-cis-splice-effects-identify-default-annotatedjunctions.out‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
11
chrom start end name score strand splice_site acceptors_skipped exons_skipped donors_skipped anchor known_donor known_acceptor known_junction gene_names gene_ids transcripts variant_info
2-
22 93668 97252 JUNC00000001 5 + GT-AG 2 1 2 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253 22:94626-94627
2+
22 93668 97252 JUNC00000001 5 + GT-AG 1 1 1 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253 22:94626-94627
33

‎tests/integration-test/data/junctions-annotate/expected-annotate.out‎

Lines changed: 41 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,43 @@
11
chrom start end name score strand splice_site acceptors_skipped exons_skipped donors_skipped anchor known_donor known_acceptor known_junction gene_names gene_ids transcripts
2-
22 14103 38192 JUNC00300575 38 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
3-
22 38307 38693 JUNC00300576 2 + GT-AG 0 0 0 N 0 0 0 NA NA NA
4-
22 38826 46869 JUNC00300577 152 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
5-
22 47045 48492 JUNC00300578 236 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
6-
22 48753 50895 JUNC00300579 299 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
7-
22 51008 52393 JUNC00300580 280 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
8-
22 51008 56818 JUNC00300581 1 + GT-AG 2 1 2 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
9-
22 52638 56818 JUNC00300582 302 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
10-
22 52642 56818 JUNC00300583 2 + GT-AG 0 0 1 A 0 1 0 EP300 ENSG00000100393 ENST00000263253
11-
22 56911 58658 JUNC00300584 340 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
12-
22 58795 61145 JUNC00300585 608 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
13-
22 61262 62053 JUNC00300586 854 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
14-
22 61262 62075 JUNC00300587 6 + GT-AG 1 0 1 D 1 0 0 EP300 ENSG00000100393 ENST00000263253
15-
22 61262 67744 JUNC00300588 1 + GT-AG 2 1 2 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
16-
22 62227 67744 JUNC00300589 1016 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
17-
22 62227 68842 JUNC00300590 28 + GT-AG 2 1 2 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
18-
22 67821 68842 JUNC00300591 1096 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
19-
22 68951 70043 JUNC00300592 971 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
20-
22 70180 70766 JUNC00300593 223 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
21-
22 71203 72838 JUNC00300594 286 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
22-
22 73017 73211 JUNC00300595 298 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
23-
22 73355 76000 JUNC00300596 217 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
24-
22 76118 78174 JUNC00300597 448 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
25-
22 78413 79417 JUNC00300598 498 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
26-
22 79505 81647 JUNC00300599 408 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
27-
22 79505 83728 JUNC00300600 1 + GT-AG 2 1 2 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
28-
22 81727 83728 JUNC00300601 348 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
29-
22 83784 85058 JUNC00300602 334 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
30-
22 85135 87604 JUNC00300603 429 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
31-
22 87671 89454 JUNC00300604 574 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
32-
22 89604 89726 JUNC00300605 572 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
33-
22 89872 90508 JUNC00300606 772 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
34-
22 90621 91411 JUNC00300607 655 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
35-
22 90621 91093 JUNC00300608 3 + GT-AG 1 0 0 D 1 0 0 EP300 ENSG00000100393 ENST00000263253
36-
22 91576 93504 JUNC00300609 387 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
37-
22 93668 94628 JUNC00300610 216 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
38-
22 94789 97252 JUNC00300611 571 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
39-
22 97533 97778 JUNC00300612 548 + GT-AG 0 0 1 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
40-
22 90586 104069 JUNC00300613 10 - GG-AG 1 0 1 A 0 1 0 RP1-85F18.6 ENSG00000232754 ENST00000415054
41-
22 90586 104068 JUNC00300614 100 - GT-AG 1 0 0 DA 1 1 1 RP1-85F18.6 ENSG00000232754 ENST00000415054
42-
22 90585 104068 JUNC00300614 10 - GT-GG 1 0 1 D 1 0 0 RP1-85F18.6 ENSG00000232754 ENST00000415054
2+
22 14103 38192 JUNC00300575 38 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
3+
22 38307 38693 JUNC00300576 2 + GT-AG 0 0 0 N 0 0 0 NA NA
4+
22 38826 46869 JUNC00300577 152 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
5+
22 47045 48492 JUNC00300578 236 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
6+
22 48753 50895 JUNC00300579 299 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
7+
22 51008 52393 JUNC00300580 280 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
8+
22 51008 56818 JUNC00300581 1 + GT-AG 1 1 1 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
9+
22 52638 56818 JUNC00300582 302 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
10+
22 52642 56818 JUNC00300583 2 + GT-AG 0 0 0 A 0 1 0 EP300 ENSG00000100393 ENST00000263253
11+
22 56911 58658 JUNC00300584 340 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
12+
22 58795 61145 JUNC00300585 608 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
13+
22 61262 62053 JUNC00300586 854 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
14+
22 61262 62075 JUNC00300587 6 + GT-AG 1 0 0 D 1 0 0 EP300 ENSG00000100393 ENST00000263253
15+
22 61262 67744 JUNC00300588 1 + GT-AG 1 1 1 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
16+
22 62227 67744 JUNC00300589 1016 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
17+
22 62227 68842 JUNC00300590 28 + GT-AG 1 1 1 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
18+
22 67821 68842 JUNC00300591 1096 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
19+
22 68951 70043 JUNC00300592 971 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
20+
22 70180 70766 JUNC00300593 223 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
21+
22 71203 72838 JUNC00300594 286 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
22+
22 73017 73211 JUNC00300595 298 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
23+
22 73355 76000 JUNC00300596 217 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
24+
22 76118 78174 JUNC00300597 448 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
25+
22 78413 79417 JUNC00300598 498 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
26+
22 79505 81647 JUNC00300599 408 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
27+
22 79505 83728 JUNC00300600 1 + GT-AG 1 1 1 NDA 1 1 0 EP300 ENSG00000100393 ENST00000263253
28+
22 81727 83728 JUNC00300601 348 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
29+
22 83784 85058 JUNC00300602 334 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
30+
22 85135 87604 JUNC00300603 429 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
31+
22 87671 89454 JUNC00300604 574 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
32+
22 89604 89726 JUNC00300605 572 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
33+
22 89872 90508 JUNC00300606 772 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
34+
22 90621 91411 JUNC00300607 655 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
35+
22 90621 91093 JUNC00300608 3 + GT-AG 0 0 0 D 1 0 0 EP300 ENSG00000100393 ENST00000263253
36+
22 91576 93504 JUNC00300609 387 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
37+
22 93668 94628 JUNC00300610 216 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
38+
22 94789 97252 JUNC00300611 571 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
39+
22 97533 97778 JUNC00300612 548 + GT-AG 0 0 0 DA 1 1 1 EP300 ENSG00000100393 ENST00000263253
40+
22 90586 104069 JUNC00300613 10 - GG-AG 0 0 1 A 0 1 0 RP1-85F18.6 ENSG00000232754 ENST00000415054
41+
22 90586 104068 JUNC00300614 100 - GT-AG 0 0 0 DA 1 1 1 RP1-85F18.6 ENSG00000232754 ENST00000415054
42+
22 90585 104068 JUNC00300614 10 - GT-GG 1 0 0 D 1 0 0 RP1-85F18.6 ENSG00000232754 ENST00000415054
4343

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