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Deal with an assert caused by a very short start exon
This fixes (imperfectly) a problem when the first exon is very short and the code detects an overflow, see test/csq/ENSCAFT00000047742 >chr9:104-110 ATGTCAGGGCC eee.eee This is not a real fix, the code would need a revamp to handle well general cases like this. However, it is not real biology, so we don't care that much. This is just so that the program does not crash on it. Fixes #2313
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6 files changed

+155
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‎csq.c‎

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -666,6 +666,7 @@ void splice_init(splice_t *splice, bcf1_t *rec)
666666
}
667667
static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
668668
{
669+
// beg .. the beggining of the splice region
669670
// len>0 .. beg is the first base, del filled from right
670671
// len<0 .. beg is the last base, del filled from left
671672

@@ -681,8 +682,24 @@ static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
681682
}
682683
else
683684
{
684-
rbeg = abeg = beg;
685-
rlen = alen = len;
685+
if ( beg < splice->tr->beg )
686+
{
687+
// This can happen with very short exons and introns. Not a real biology, but the program
688+
// should not crash on it. This is not a real fix, the code would need a revamp to handle
689+
// well cases like this, see test/csq/ENSCAFT00000047742
690+
// >chr9:104-110
691+
// ATGTCAGGGCC
692+
// ATGTC-GGGCC
693+
// 456
694+
// eee.eee
695+
rbeg = abeg = splice->tr->beg;
696+
rlen = alen = 0;
697+
}
698+
else
699+
{
700+
rbeg = abeg = beg;
701+
rlen = alen = len;
702+
}
686703
// check for incomplete del as above??
687704
}
688705

‎test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa‎

Lines changed: 114 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,114 @@
1+
>chr9 chr9:19518647-19527624
2+
GCGGGACGGGGCGGTCCCCGCTCGGAGCCCCCGCCCAGCTGACCCGGCGGCTCTCCCCTCGCAGGCTGCTGCCCCGGCGT
3+
GCAGGGCCCGGCCGCCGCCATGTCAGGGCCCGTTCGAGCTCTCGGTGCAGGACCTCAACGACCTGCTGTCGGACGGCAGC
4+
GGCTGTTACAGCCTGCCGAGCCAGCCTTGCAAGGAGGTCACCCCCAGGATCTACGTGGGCAACGCGTGAGTCGCCGTTGG
5+
GGCGCCCCGCCCACCCGAAAGCCGGGGTCGGGGCGTTGCGGGcgctggggggggggtgcggggcgTGGCCGCCCTCCGGG
6+
AGCCCCGCGGGGCCGGGCAGGGGCTGGAGTCGCCGCCCGCCCCCGCGCAGTGGGGCGGAGGGGCTAgaccccgccccggc
7+
cccgcgcgTCCTCCCCCCGCGGGGGGCCCGGGTCCCCGGGCGTCCGGCCCGAAGCCGCCAGCCGCTAGGGGCTTGGCCTT
8+
GGGCGGGGTCGGGCTACCGGGATCACTTAACAGGTGGCCCTCTGTCACCCGGCCGGTCTCCAGCCCGCGCGTCATGTGAC
9+
ATCTGCCTGGTTCTGCAGTGAGGTCACCGCGGAATGTCTGCCTTCGCTGCCATGGCAACTGGCTGACGTCACAGATCGGG
10+
CGTGGAACTTTCCCGGCTGGGCAGGCCAGATCAAGGAATCGAAATACTCCCAATGAGGGATCCGGAGAGCTGGGCTGGGG
11+
TTTCCTtgctccctcccctgccttccaGATAGGGTTTGGTTTACCAACGCCCTAAGTTCCATGGGCCAGGGTCTGCGTTA
12+
GAAACCCAGAACTAACTCCCTTCTCCCCTTTGACCCAGGAGGAAATGGTGGCCCAGGGTGGTTGAGGGACTGTGAGGACA
13+
GAGACCATGCCTTGTTCATGTCTGTATCCCCTGTCCTGTACTAGGACCTGCTGCTTACCCTGCTAAGGGCTGCCACAAAA
14+
ATGAGGGTCATCGCGGGGCAAGAAGGGGTCCCTAAGGCAGGTCCTGCCTTCGTGGGGACTGTCTCATCcattccatccat
15+
tcattcaccatattgagcacctactgtgtgtccgGCATTTACAGTGCACATTCATAGTGATAGTAGTGGTAACGGTAAAT
16+
TTGTTGAACGCTGAATTAGAGAAGGGAGGTGAATGAAAATTCACCTTcagagttatttgtttttttaatcaaccaCTGTT
17+
TAACAACCACGTGCAGTGTCATGAGCAGGAACAGCTGAAACAGTCCCAGGGCCTTAGCCGAAGTGCTCCGTAATTGCAAA
18+
GTTCAGAGGATAGTGCTCTGTCCAGCCACCCCAGCAGCAAGTGGCCTTGGTGCCTCGGAGAACCCGCTGTCTGGGGCAGT
19+
TTGGCACATTCAGCTGCCCCTCCTTCCCGAGTGGAAACCGAGGCGGTGGATGTCTGGTGGTAGCCAGGGTGGAAAGTGCC
20+
GGTGGCCACTGTAGAGAAACACATCCCCAGCCCAATTAGTGAATCTGGCTTTGACTTGaccaggggtgtgggggggtaCT
21+
CCTGCACATAGGGAGCCCCTGAACCAAATCAGGGCTCACAGGGCCTGGAGAGGAGTCTGTATGAGCCTCATTTTCTAGAT
22+
CTCAGGATCTGCAGTTGATGTGGACATGCCAGGCAGAGTGAGGGGAAGACAGAGCAGGGCTGGTGTCAGGTCTTCTCCTT
23+
GCTCTGCCCCTAAGCATCCCATGTGAGCCCCAGCACTGTCCTTCCACTGTCCTGGAAGCTTAAGCCCAGGCCTGGCTTCC
24+
TTGCAGGCTGCTGTGACAGGCAAACAAGATCATGTCGGAGAAGGCACTTTGTAAAGTATAAACTGTTGTCTGAATTGGGA
25+
TGTTGTTGGGAGATGAAATAAAGGAGCCCTTTGACTATTCAGATCAAATGTTTTATAACCCCCAGAGTTCTGTTGGCGCC
26+
ACTTGGTCCCCAAGTGCTTACTCACCCAGGGGAGCTTCAGAAATGTGGCTAGTGGTCTGTGGTGGAAAGGGCCCCTCTGG
27+
GGGACTGGAGGGGCCGCCACACTTTATAGTCCAAGGAAGGAGGCTGCCTAAGATGTgttgatttcattctttctcactgA
28+
TTCACCCCATAGTCATTCAGCACCTATAGCCGGGTGCAATAGCAAGTGCTGGGCAGACAGACCTGGTTACCCCCTCAAAA
29+
GTTCACAGCCTACCCATCCGAACAAATAATCACAATCAGGCATTAGAAGAGCACTGACTACGGTGTCAAGCTCTGTCTAT
30+
AGgctagatcattttttttttttttaaatttttatttatttatgatagtcacagagagagagagagagaggcagagacac
31+
aggcagagggagaaacaggctccatgcaccgggagcccgacgtgggattcgatcctgcgtctccaggatcgcgccctggg
32+
ccaaaggcaggcgccaaaccgctgcgccacccagggatccctaggctaGATCATTTAATCCTTCTGCCCAGGGGGTAGGT
33+
ATTGTTGTCAACCTCATTtgacagatagggaaactgagtcaccaaAAGGTTAAGTGGCTTGCTTAAGGTTACCTGGCTGG
34+
CAAGTCTCAGGGTTCGACTCagacccaggcagtctgactctagAGCCCGTTTTGAGCCAGTAGGCTGTACCACCACCACA
35+
GTATAGGGAACATGATGCCAGATGGAATGGAGGGGGCGATCAGGGCATATTGATGGAAAATGAGAGGGTGTGTGACCATG
36+
GAGAAGCTCGAGAAGGGCATTCCagggagagggaacagcatgggGCTGAAACCACCCCAGCTATTTGGGGAAGCTGCTGG
37+
TAATTAGATATGGCTGGAGTAAGGGAGGTGGGTCACAAGATGAGGGGAAGTTGGCAGGGGCCAAGCGTGGAGGCTTCCTC
38+
GCTTTGCCAGGAGACTTAGaatcttctccatcttcctccttcTGGGGCTGCCAGGTGGTCAGGTAATCATCCCCCTGCTC
39+
CTGTCTCCTGTCCAGGTCTGTGGCTCAAGACATCCCCAAGCTGCAGAAACTAGGCATCACCCATGTTCTGAATGCTGCTG
40+
AGGGCAGGTCCTTCATGCACGTCAACACCAATGCCAACTTCTACAAGGACTCCGGCattacctacctgggcatcaagGCC
41+
AATGACACGCAGGAGTTCAACCTCAGCGCCTACTTTGAAAGGGCTGCAGACTTCATCGACCAGGCCCTGGCTCAAAAGAA
42+
TGGTAAGGCACATGTGGCCCAGGAAACAGTGCAAGGCAGTTctgactggatttttttctagaaaacagGCCCACAACTGG
43+
CTTCCTCTTGGAAAACCTATCAAGTGGCCACATGTTACACAAGATTTATAAATGTTTCTCACCATGGCAGCCCCGGGGTC
44+
CTTGGGTTTGAGTGGACTTTGCCTGAGAGTTCCTTTCTAGCCACTCCCCGCCATGCCCTCAGTTCAAATAGCTTTAGTAA
45+
TAATGATTTTATCTTCCATGATAAGAAGTCCTGAGGTGAGGGAGCTCTGGGGCTGGTTGATTCAGCAGCTTGGTGGCGAC
46+
ATCAGGAAGAGGTGCTTCCCTTTTCTCTTGCACGCCACCCTCAGGGTTCTCCCCTCATGGTCCCAAGATGGCGGTGGTAG
47+
ACCTAGTCACCACATCCTAGCAGAACAAAGCATAGCAAAAGACCAGGCAGCCATCTCTTCCTtgtgtttcttcccttttt
48+
ttaatgagcaagtaaaagggtgcctgagtggctcagtcggttgagggtctgccatcagctcaggtcatgatctcaggttc
49+
ctgagattgagccctatatggagctctctgctcagtggggagtctgcatctccctcttctctgttcctctgcctgGCTCG
50+
TGctcggtttctctctctctcaaataaataaataaaaataaagagcaagtAGAAGGGTGCTCAGAAACCCTTCATTGGGG
51+
TTCCCCTCACATCTCAGTGGCTGAATTGGCTTACATGAACGCCTGGCCAGGGAAACAGGGCAGCCATGACTGGCTTAGGC
52+
GGGTGCTTAGCAAGCTGTGGCCCACAGACCACATCTTCCAGCCACTTTCTAAATGCTTCCTGCAGCACCCAAATCTAAGA
53+
CTGAGCAGAACTGCTGAGTTGCtggcaggcagggaggcaggaccTCCCTGGGGGAAACCCTAGAAGGCAGAGGGCAAACG
54+
TCAGTTGAGCAGGCTGGGCCACTTGCCCTTTCCCTTTTAGCTTGTTTCTCTCAGCGCCTGCCTTTACCTTCAAGCTGCCT
55+
CCCCTGgcctcttcctccctcaccaCGGCCTTCTCAGGGGAAGTGAGCCCCATGAAGGTATGATCAGCCTTGATACCCTG
56+
ATTCtagcctgtctctgcttcttgtGCCCAACAGCCTCCCCCTGGAATGATTTCCAGTGAACAGTGTGTACTAGATGCTG
57+
GTTATCGCATATCTGGGGCTCAGGAGGGAAGTTTTATTGCCCGGGGAATCTGCAACTTTACTGTAAGGCCCTTTGTGGTC
58+
CTTCATGATCTTGTGTGTGTCACCCCCGCCATTCCGGCTATATTGGGTTCCTGTGTTGATGGGAACGAGGGGCCCAGTTA
59+
AGGGGATGGATTTTGCTCTTCTTGTATGTGGGTTGGTCATCCGCTTAAGGAACTTAGAGCTTCCTGACTTTGTTTCCTCT
60+
CTCCATACAACTGGGAACATACCTTGGCTTTTTGTGACCTCTCGCCTCAGCAGGAGGCAGCATGGGCTGAGTTTTCAGTC
61+
TGGAaagttctctctgcttctccctatcttGTCCCCTGGCAAATTCCACCTTGTGCTTTAACCCTGGGCATAGTGTTCTC
62+
TCTTCCATGAAGCCTGCCCTCAGTTGGGTCCACTGTGTCCCCTTCTGTCTCCCCAGCACCTGATGCAGCATTGGGCACAT
63+
AGCAGACATGCTGCAAATAATTACTGAGTGAGTGACAAAAATGAATTCCATGGGCTCTAATGCCAAGTGTACATGCTTCT
64+
AGGATTGACTGGCCAAGCGAGTCAACAGAAACACACTGGCCTCCTGCAGTGTGCAGGGCTCAGGAGAGCCAGATGCCCAT
65+
CACTTTGGAGAAGGGGAAACAGCCAGGAGTGCTCAGAGGAGAAAGCAGTCACTTCTAGCCAGGAAGGTCAAGGGACACTT
66+
TTATGGAGGACATGGCATCTGAGTGGGCCCTGGAAGGATGGGAGTCAAACCTTCCTCTTCCCCATTGTCTCTGTGAGCCC
67+
TGGACTGCTAAATATGTTCCAGGTGGTGAGGCAGGGAAAGCCCCACTTTGCATACTTTCAGTATACTGGCTAGAGAGGGA
68+
ACTGGCAGGAAAGTGGAGGGCTCCCCCTTCCTGCTTGGAAGGCACGGGGAAAGAGAGTCATGTTTTGGGGGCAGGGTGAT
69+
GGGAACACAAGAGACTTTGGGCTAGCAGATTTCCTCCAGGATAATGGCAGTATTTAGGCATTGGTGGATAATCATCCACT
70+
TGGCTagtgagcaaatatttattgagcaccaagtGCATACTAGAGGTTGTAGGGTATCCTAAAATCAATACCACACTGTC
71+
CTTGCCCATTACATAAGCCAAGCATTAGCCTAAGGGCTTTATGTGACGTTTCCTTCAATCCCCTAACAACACTGTGCAAT
72+
GGATACTATTAACACAGATGATGAATCGAGGCATAGGTGGGTTAGGTGGGTCTTAGGGTTCATAACCAGTAAATTGgcca
73+
ggaaggaaaagagaaccaATAGAATAAAcagatattttaaggaattgtcTTATACAATTGTAGGATCTGGCAAATCTGAA
74+
ATCTGTGGGGTAGAGTGGTAGGCTGGAAACTCGGGCAGGGCTTCTTGATTACAGCCTTGAGGcagaatttctctttctcc
75+
agtgaACCTCACATTTTGCTCTTAAGATCTTtgactgattggatgaggcctaaACACATTATCAAGGGTGATCTCCTTTA
76+
CTAAAAGTCAACTGATAGTCTGTGTTAATTACATTCACAAAATACCTTATAGACTAGTGTTTGACCAAGCAGCTGAGCAT
77+
CATAGACAAGCCAGGCTGACAAATGGAACCATCAGAACCAGTAAGTTAGAATTTAAACCCACATTCATAGgacttcaaag
78+
attttttttttttttttttttttttttaagatttattttctggggcacctgcatggcttagtcagttgagcattccactc
79+
ttggttttggctcaggtcataatcttaggttTGGGAAATCGAACCCTGCCtcagtctctgcactcagcagggagtctgct
80+
ttccctctccctctgcctctgctaccacttccccccaccccacctcctaaCCACCACCCTTCTCTGGcttctgcaaaata
81+
tatatatatatatatatatatatatatatatatatatatatatatatttatttgagagagagagagtgtgtgcacatgtg
82+
cacatgagtgaggtggggggagggggaaaggggaggCTTGgtacagggctccatctcaggactctcaGACCATGACAtga
83+
accaaaattaagagtcagaggcttaaccgactgagccacccagatgccccaaagatTTTGGTTCTAAATCCCTAtgctga
84+
aaaaggaaatatttgaactGGGGTTTTAAGGGATGACAGGAATTTGCCAGGTGGCCGAGAGAGACTTTGTTCCCTATAGA
85+
GGAAATGACTTGTGGAAAGGCACCAGGGGTAGGGAAAAGCATGGGAACGTATCAAGGCCGTGGGTACTTGGCCTTGTAAG
86+
CCACTCCTTGGAGACAAGAAGCCCTGCAAATGGTGATAGgttttatttgaatatagaaaGCCCCTTCCTGCTGCTAGGTA
87+
GAGGGTGAATTGGTGATGATGAGGGTAGATCAAGAGCTCAGTTTGGAGGTGTGAAGAGGGTGGAGGTGAGGGTGATGAGG
88+
ACCTGAACTAACACTCTGTGGCCTGAGTGGGTGGTGGCAGAGAGAAGCCGAGGCTTGGGGCTCTTGGGGACCCCTGGTGG
89+
AAATGAAATGTGCTGGGACTTGTTGATGCTCTCTTTCACCAAATGCTGGGGATGCAGCAGGGAGCCAAACAGACAATTCT
90+
GCCTTGTGGAGCTTTTCCATCTCAGGGGAAGCTGACAGCAAACAAGTGAAGATTTCTGGCCTGGGGCcaggcggggggga
91+
ggggcgggtggGCGAAAGCAGGGAGTCAGGGATGAGAGAGGAGAAGGGCTGGGAGTGGGTTTGAGGCTTTAGAGAGGCTG
92+
AGTGGGAGAGCAAACACCTGGGGAGAGAGGTTTGCAAGCTGAGAAGCCAGCTGGCTGgtgaagggatggagggagagagg
93+
agacaatgtaggggcggggaggggggggtgcaGATTTTATAGGGCCTCGCGGGCCATTTGGGGAGCCGTGAGCAGGTGtt
94+
tatatttacatgttttgatatttttatccTCCTGTTTGTATTTGACATGCAcgttccttttactttttaaaccactttgt
95+
tgagttataattgacattCAACACATTTAAACATCACACATTTAAAGCCTGCAGTTTGACATTTTGACTTCTGTGTATAC
96+
CTGTGAAACCAGGACCACAAACGAGAGTGTGAGCACACCCGTCTCGCCCCAGGCGCCTCTGTGGCCTCTCCCTTCCGCTC
97+
CTTCTGCCTCCCATTTCTAAGCAACTGCCGCTCTGTTTTCTGTCACCAGACACAAGTGTACATTTTGTGGACTTTTGTGT
98+
AAATGGAATTACACAGTGGGTGTGCTTTCTTGGCCTGGCCTCTGCCGGTGTCATTGCTGTGAGTTCCATCTCGGTCACTA
99+
CACGTGTCCATAGCTCATTCCTGTTTAATGCTGACGAACCTTCCAGTGTATGGATGTGTCCCAGTTTGTGTGTTCACCTA
100+
TTGGTGAacttttggattatttctatgttttctttttttgttttttgtttttttactttatttagttatttgataGAGGC
101+
AGTGgggagcatgagccaggggaggagcagagggagaagcagactccccactgaacagggagcccgacgccaggcttgat
102+
cccaggaccccaggatcatgacctgagctgaagacagatgcttaatggaccGAGCCACTGTATGTTTTGCTTttgattga
103+
aatataaaattcacgTGGAGAAATGCTGGTATCACAAGTGTGCAGATCAGTGTGTTGCcctcagatcaagaaatagatCT
104+
CCCCCCCAGGACTCTAGAAACCCCTAGTGTGTTCCCTCCCTATCTCACTGTTACTACCACCCAGACTTCTGTTAGCGCAG
105+
AGCAGTTCTGCTTGCCCTCCTATTCCATGAACTCACAAATGtcctatgtgtgtgtctcatccGTGTTCTAAGTGTAAGTC
106+
GTACACTGTTTATCGGTCCTGCCGTTGAAGGGCCTCTGGGAGCTGCCAGCTGGGGCCACTAGGAACAGTGCTGCCCTATG
107+
AATATTCTGGTGCGTGTCTTTGGTGGACATGCATGCACctccctgctgggccctgggggttgCATGTGTCAACCTGAGTA
108+
CGTACTGCCCTGTGGTTCGCCAGAGCCATGTGCTCACGTACACTGCCCCCTGCACAGCCACAGATAGAAGtcctgctgct
109+
ccacatcctcgcTGATGCTTTGTGTTTTCCGTCTTCTCCATCCGGGCGGGTACACAATGGCCTCTTGTACTTTTCATTTG
110+
CGCTTCCCCCGGAAGAGTTCTGACTCGAGTCGGGCTGTGTTGGGATGGCCCCAGCTCACGCTCCCTCGTCCCTGTCTCTT
111+
TCAGGCCGGGTCCTTGTCCACTGCCGGGAAGGTTACAGCCGCTCCCCAACCCTAGTTATCGCGTACCTCATGATGCGGCA
112+
GAAGATGGATGTCAAGTCTGCCCTGAGCATCGTGAGGCAGAACCGTGAGATCGGCCCCAACGATGGTTTCCTGGCCCAGC
113+
TATGCCAGCTCAATGACAAACTAGTCAAGGAGGGGAAATTGAAACTCTAGGGCACTCCCGCTGCCTCTTCTCTAGCGGCA
114+
GACAGGGGAGGCCCTGGT

‎test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa.fai‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
chr9 8978 29 80 81

‎test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff‎

Lines changed: 11 additions & 0 deletions
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1+
chr9 ensembl gene 100 8978 . + . ID=gene:ENSCAFG00000028570;Name=DUSP3;biotype=protein_coding;description=dual specificity phosphatase 3 [Source:VGNC Symbol%3BAcc:VGNC:53236];gene_id=ENSCAFG00000028570;logic_name=ensembl;version=2
2+
chr9 ensembl mRNA 100 8978 . + . ID=transcript:ENSCAFT00000047742;Parent=gene:ENSCAFG00000028570;Name=DUSP3-201;biotype=protein_coding;transcript_id=ENSCAFT00000047742;version=2
3+
chr9 ensembl exon 100 104 . + . Parent=transcript:ENSCAFT00000047742;Name=ENSCAFE00000400429;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=ENSCAFE00000400429;rank=1;version=1
4+
chr9 ensembl CDS 100 104 . + 0 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
5+
chr9 ensembl exon 106 225 . + . Parent=transcript:ENSCAFT00000047742;Name=ENSCAFE00000157884;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSCAFE00000157884;rank=2;version=4
6+
chr9 ensembl CDS 106 225 . + 1 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
7+
chr9 ensembl exon 2976 3202 . + . Parent=transcript:ENSCAFT00000047742;Name=ENSCAFE00000157890;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=ENSCAFE00000157890;rank=3;version=1
8+
chr9 ensembl CDS 2976 3202 . + 1 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
9+
chr9 ensembl CDS 8725 8930 . + 2 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
10+
chr9 ensembl exon 8725 8978 . + . Parent=transcript:ENSCAFT00000047742;Name=ENSCAFE00000307165;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=ENSCAFE00000307165;rank=4;version=2
11+
chr9 ensembl three_prime_UTR 8931 8978 . + . Parent=transcript:ENSCAFT00000047742

‎test/csq/ENSCAFT00000047742/test.txt‎

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1+
104 CA C synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
2+
104 CA C synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
3+

‎test/csq/ENSCAFT00000047742/test.vcf‎

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1+
##fileformat=VCFv4.2
2+
##contig=<ID=chr9,length=249250621>
3+
##INFO=<ID=type,Number=.,Type=String,Description="">
4+
##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
5+
##INFO=<ID=EXPL,Number=1,Type=String,Description="Expected consequence with bt/csq -l">
6+
#CHROM POS ID REF ALT QUAL FILTER INFO
7+
chr9 104 . CA C . PASS EXP=synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding

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