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Deal with an assert caused by a very short start exon
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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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@pd3
pd3 committed Dec 1, 2024
1 parent a5bc0ea commit b29c54c
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Showing 6 changed files with 155 additions and 2 deletions.
21 changes: 19 additions & 2 deletions csq.c
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Original file line number Diff line number Diff line change
Expand Up @@ -666,6 +666,7 @@ void splice_init(splice_t *splice, bcf1_t *rec)
}
static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
{
// beg .. the beggining of the splice region
// len>0 .. beg is the first base, del filled from right
// len<0 .. beg is the last base, del filled from left

Expand All @@ -681,8 +682,24 @@ static inline void splice_build_hap(splice_t *splice, uint32_t beg, int len)
}
else
{
rbeg = abeg = beg;
rlen = alen = len;
if ( beg < splice->tr->beg )
{
// This can happen with very short exons and introns. Not a real biology, but the program
// should not crash on it. This is not a real fix, the code would need a revamp to handle
// well cases like this, see test/csq/ENSCAFT00000047742
// >chr9:104-110
// ATGTCAGGGCC
// ATGTC-GGGCC
// 456
// eee.eee
rbeg = abeg = splice->tr->beg;
rlen = alen = 0;
}
else
{
rbeg = abeg = beg;
rlen = alen = len;
}
// check for incomplete del as above??
}

Expand Down
114 changes: 114 additions & 0 deletions test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa
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@@ -0,0 +1,114 @@
>chr9 chr9:19518647-19527624
GCGGGACGGGGCGGTCCCCGCTCGGAGCCCCCGCCCAGCTGACCCGGCGGCTCTCCCCTCGCAGGCTGCTGCCCCGGCGT
GCAGGGCCCGGCCGCCGCCATGTCAGGGCCCGTTCGAGCTCTCGGTGCAGGACCTCAACGACCTGCTGTCGGACGGCAGC
GGCTGTTACAGCCTGCCGAGCCAGCCTTGCAAGGAGGTCACCCCCAGGATCTACGTGGGCAACGCGTGAGTCGCCGTTGG
GGCGCCCCGCCCACCCGAAAGCCGGGGTCGGGGCGTTGCGGGcgctggggggggggtgcggggcgTGGCCGCCCTCCGGG
AGCCCCGCGGGGCCGGGCAGGGGCTGGAGTCGCCGCCCGCCCCCGCGCAGTGGGGCGGAGGGGCTAgaccccgccccggc
cccgcgcgTCCTCCCCCCGCGGGGGGCCCGGGTCCCCGGGCGTCCGGCCCGAAGCCGCCAGCCGCTAGGGGCTTGGCCTT
GGGCGGGGTCGGGCTACCGGGATCACTTAACAGGTGGCCCTCTGTCACCCGGCCGGTCTCCAGCCCGCGCGTCATGTGAC
ATCTGCCTGGTTCTGCAGTGAGGTCACCGCGGAATGTCTGCCTTCGCTGCCATGGCAACTGGCTGACGTCACAGATCGGG
CGTGGAACTTTCCCGGCTGGGCAGGCCAGATCAAGGAATCGAAATACTCCCAATGAGGGATCCGGAGAGCTGGGCTGGGG
TTTCCTtgctccctcccctgccttccaGATAGGGTTTGGTTTACCAACGCCCTAAGTTCCATGGGCCAGGGTCTGCGTTA
GAAACCCAGAACTAACTCCCTTCTCCCCTTTGACCCAGGAGGAAATGGTGGCCCAGGGTGGTTGAGGGACTGTGAGGACA
GAGACCATGCCTTGTTCATGTCTGTATCCCCTGTCCTGTACTAGGACCTGCTGCTTACCCTGCTAAGGGCTGCCACAAAA
ATGAGGGTCATCGCGGGGCAAGAAGGGGTCCCTAAGGCAGGTCCTGCCTTCGTGGGGACTGTCTCATCcattccatccat
tcattcaccatattgagcacctactgtgtgtccgGCATTTACAGTGCACATTCATAGTGATAGTAGTGGTAACGGTAAAT
TTGTTGAACGCTGAATTAGAGAAGGGAGGTGAATGAAAATTCACCTTcagagttatttgtttttttaatcaaccaCTGTT
TAACAACCACGTGCAGTGTCATGAGCAGGAACAGCTGAAACAGTCCCAGGGCCTTAGCCGAAGTGCTCCGTAATTGCAAA
GTTCAGAGGATAGTGCTCTGTCCAGCCACCCCAGCAGCAAGTGGCCTTGGTGCCTCGGAGAACCCGCTGTCTGGGGCAGT
TTGGCACATTCAGCTGCCCCTCCTTCCCGAGTGGAAACCGAGGCGGTGGATGTCTGGTGGTAGCCAGGGTGGAAAGTGCC
GGTGGCCACTGTAGAGAAACACATCCCCAGCCCAATTAGTGAATCTGGCTTTGACTTGaccaggggtgtgggggggtaCT
CCTGCACATAGGGAGCCCCTGAACCAAATCAGGGCTCACAGGGCCTGGAGAGGAGTCTGTATGAGCCTCATTTTCTAGAT
CTCAGGATCTGCAGTTGATGTGGACATGCCAGGCAGAGTGAGGGGAAGACAGAGCAGGGCTGGTGTCAGGTCTTCTCCTT
GCTCTGCCCCTAAGCATCCCATGTGAGCCCCAGCACTGTCCTTCCACTGTCCTGGAAGCTTAAGCCCAGGCCTGGCTTCC
TTGCAGGCTGCTGTGACAGGCAAACAAGATCATGTCGGAGAAGGCACTTTGTAAAGTATAAACTGTTGTCTGAATTGGGA
TGTTGTTGGGAGATGAAATAAAGGAGCCCTTTGACTATTCAGATCAAATGTTTTATAACCCCCAGAGTTCTGTTGGCGCC
ACTTGGTCCCCAAGTGCTTACTCACCCAGGGGAGCTTCAGAAATGTGGCTAGTGGTCTGTGGTGGAAAGGGCCCCTCTGG
GGGACTGGAGGGGCCGCCACACTTTATAGTCCAAGGAAGGAGGCTGCCTAAGATGTgttgatttcattctttctcactgA
TTCACCCCATAGTCATTCAGCACCTATAGCCGGGTGCAATAGCAAGTGCTGGGCAGACAGACCTGGTTACCCCCTCAAAA
GTTCACAGCCTACCCATCCGAACAAATAATCACAATCAGGCATTAGAAGAGCACTGACTACGGTGTCAAGCTCTGTCTAT
AGgctagatcattttttttttttttaaatttttatttatttatgatagtcacagagagagagagagagaggcagagacac
aggcagagggagaaacaggctccatgcaccgggagcccgacgtgggattcgatcctgcgtctccaggatcgcgccctggg
ccaaaggcaggcgccaaaccgctgcgccacccagggatccctaggctaGATCATTTAATCCTTCTGCCCAGGGGGTAGGT
ATTGTTGTCAACCTCATTtgacagatagggaaactgagtcaccaaAAGGTTAAGTGGCTTGCTTAAGGTTACCTGGCTGG
CAAGTCTCAGGGTTCGACTCagacccaggcagtctgactctagAGCCCGTTTTGAGCCAGTAGGCTGTACCACCACCACA
GTATAGGGAACATGATGCCAGATGGAATGGAGGGGGCGATCAGGGCATATTGATGGAAAATGAGAGGGTGTGTGACCATG
GAGAAGCTCGAGAAGGGCATTCCagggagagggaacagcatgggGCTGAAACCACCCCAGCTATTTGGGGAAGCTGCTGG
TAATTAGATATGGCTGGAGTAAGGGAGGTGGGTCACAAGATGAGGGGAAGTTGGCAGGGGCCAAGCGTGGAGGCTTCCTC
GCTTTGCCAGGAGACTTAGaatcttctccatcttcctccttcTGGGGCTGCCAGGTGGTCAGGTAATCATCCCCCTGCTC
CTGTCTCCTGTCCAGGTCTGTGGCTCAAGACATCCCCAAGCTGCAGAAACTAGGCATCACCCATGTTCTGAATGCTGCTG
AGGGCAGGTCCTTCATGCACGTCAACACCAATGCCAACTTCTACAAGGACTCCGGCattacctacctgggcatcaagGCC
AATGACACGCAGGAGTTCAACCTCAGCGCCTACTTTGAAAGGGCTGCAGACTTCATCGACCAGGCCCTGGCTCAAAAGAA
TGGTAAGGCACATGTGGCCCAGGAAACAGTGCAAGGCAGTTctgactggatttttttctagaaaacagGCCCACAACTGG
CTTCCTCTTGGAAAACCTATCAAGTGGCCACATGTTACACAAGATTTATAAATGTTTCTCACCATGGCAGCCCCGGGGTC
CTTGGGTTTGAGTGGACTTTGCCTGAGAGTTCCTTTCTAGCCACTCCCCGCCATGCCCTCAGTTCAAATAGCTTTAGTAA
TAATGATTTTATCTTCCATGATAAGAAGTCCTGAGGTGAGGGAGCTCTGGGGCTGGTTGATTCAGCAGCTTGGTGGCGAC
ATCAGGAAGAGGTGCTTCCCTTTTCTCTTGCACGCCACCCTCAGGGTTCTCCCCTCATGGTCCCAAGATGGCGGTGGTAG
ACCTAGTCACCACATCCTAGCAGAACAAAGCATAGCAAAAGACCAGGCAGCCATCTCTTCCTtgtgtttcttcccttttt
ttaatgagcaagtaaaagggtgcctgagtggctcagtcggttgagggtctgccatcagctcaggtcatgatctcaggttc
ctgagattgagccctatatggagctctctgctcagtggggagtctgcatctccctcttctctgttcctctgcctgGCTCG
TGctcggtttctctctctctcaaataaataaataaaaataaagagcaagtAGAAGGGTGCTCAGAAACCCTTCATTGGGG
TTCCCCTCACATCTCAGTGGCTGAATTGGCTTACATGAACGCCTGGCCAGGGAAACAGGGCAGCCATGACTGGCTTAGGC
GGGTGCTTAGCAAGCTGTGGCCCACAGACCACATCTTCCAGCCACTTTCTAAATGCTTCCTGCAGCACCCAAATCTAAGA
CTGAGCAGAACTGCTGAGTTGCtggcaggcagggaggcaggaccTCCCTGGGGGAAACCCTAGAAGGCAGAGGGCAAACG
TCAGTTGAGCAGGCTGGGCCACTTGCCCTTTCCCTTTTAGCTTGTTTCTCTCAGCGCCTGCCTTTACCTTCAAGCTGCCT
CCCCTGgcctcttcctccctcaccaCGGCCTTCTCAGGGGAAGTGAGCCCCATGAAGGTATGATCAGCCTTGATACCCTG
ATTCtagcctgtctctgcttcttgtGCCCAACAGCCTCCCCCTGGAATGATTTCCAGTGAACAGTGTGTACTAGATGCTG
GTTATCGCATATCTGGGGCTCAGGAGGGAAGTTTTATTGCCCGGGGAATCTGCAACTTTACTGTAAGGCCCTTTGTGGTC
CTTCATGATCTTGTGTGTGTCACCCCCGCCATTCCGGCTATATTGGGTTCCTGTGTTGATGGGAACGAGGGGCCCAGTTA
AGGGGATGGATTTTGCTCTTCTTGTATGTGGGTTGGTCATCCGCTTAAGGAACTTAGAGCTTCCTGACTTTGTTTCCTCT
CTCCATACAACTGGGAACATACCTTGGCTTTTTGTGACCTCTCGCCTCAGCAGGAGGCAGCATGGGCTGAGTTTTCAGTC
TGGAaagttctctctgcttctccctatcttGTCCCCTGGCAAATTCCACCTTGTGCTTTAACCCTGGGCATAGTGTTCTC
TCTTCCATGAAGCCTGCCCTCAGTTGGGTCCACTGTGTCCCCTTCTGTCTCCCCAGCACCTGATGCAGCATTGGGCACAT
AGCAGACATGCTGCAAATAATTACTGAGTGAGTGACAAAAATGAATTCCATGGGCTCTAATGCCAAGTGTACATGCTTCT
AGGATTGACTGGCCAAGCGAGTCAACAGAAACACACTGGCCTCCTGCAGTGTGCAGGGCTCAGGAGAGCCAGATGCCCAT
CACTTTGGAGAAGGGGAAACAGCCAGGAGTGCTCAGAGGAGAAAGCAGTCACTTCTAGCCAGGAAGGTCAAGGGACACTT
TTATGGAGGACATGGCATCTGAGTGGGCCCTGGAAGGATGGGAGTCAAACCTTCCTCTTCCCCATTGTCTCTGTGAGCCC
TGGACTGCTAAATATGTTCCAGGTGGTGAGGCAGGGAAAGCCCCACTTTGCATACTTTCAGTATACTGGCTAGAGAGGGA
ACTGGCAGGAAAGTGGAGGGCTCCCCCTTCCTGCTTGGAAGGCACGGGGAAAGAGAGTCATGTTTTGGGGGCAGGGTGAT
GGGAACACAAGAGACTTTGGGCTAGCAGATTTCCTCCAGGATAATGGCAGTATTTAGGCATTGGTGGATAATCATCCACT
TGGCTagtgagcaaatatttattgagcaccaagtGCATACTAGAGGTTGTAGGGTATCCTAAAATCAATACCACACTGTC
CTTGCCCATTACATAAGCCAAGCATTAGCCTAAGGGCTTTATGTGACGTTTCCTTCAATCCCCTAACAACACTGTGCAAT
GGATACTATTAACACAGATGATGAATCGAGGCATAGGTGGGTTAGGTGGGTCTTAGGGTTCATAACCAGTAAATTGgcca
ggaaggaaaagagaaccaATAGAATAAAcagatattttaaggaattgtcTTATACAATTGTAGGATCTGGCAAATCTGAA
ATCTGTGGGGTAGAGTGGTAGGCTGGAAACTCGGGCAGGGCTTCTTGATTACAGCCTTGAGGcagaatttctctttctcc
agtgaACCTCACATTTTGCTCTTAAGATCTTtgactgattggatgaggcctaaACACATTATCAAGGGTGATCTCCTTTA
CTAAAAGTCAACTGATAGTCTGTGTTAATTACATTCACAAAATACCTTATAGACTAGTGTTTGACCAAGCAGCTGAGCAT
CATAGACAAGCCAGGCTGACAAATGGAACCATCAGAACCAGTAAGTTAGAATTTAAACCCACATTCATAGgacttcaaag
attttttttttttttttttttttttttaagatttattttctggggcacctgcatggcttagtcagttgagcattccactc
ttggttttggctcaggtcataatcttaggttTGGGAAATCGAACCCTGCCtcagtctctgcactcagcagggagtctgct
ttccctctccctctgcctctgctaccacttccccccaccccacctcctaaCCACCACCCTTCTCTGGcttctgcaaaata
tatatatatatatatatatatatatatatatatatatatatatatatttatttgagagagagagagtgtgtgcacatgtg
cacatgagtgaggtggggggagggggaaaggggaggCTTGgtacagggctccatctcaggactctcaGACCATGACAtga
accaaaattaagagtcagaggcttaaccgactgagccacccagatgccccaaagatTTTGGTTCTAAATCCCTAtgctga
aaaaggaaatatttgaactGGGGTTTTAAGGGATGACAGGAATTTGCCAGGTGGCCGAGAGAGACTTTGTTCCCTATAGA
GGAAATGACTTGTGGAAAGGCACCAGGGGTAGGGAAAAGCATGGGAACGTATCAAGGCCGTGGGTACTTGGCCTTGTAAG
CCACTCCTTGGAGACAAGAAGCCCTGCAAATGGTGATAGgttttatttgaatatagaaaGCCCCTTCCTGCTGCTAGGTA
GAGGGTGAATTGGTGATGATGAGGGTAGATCAAGAGCTCAGTTTGGAGGTGTGAAGAGGGTGGAGGTGAGGGTGATGAGG
ACCTGAACTAACACTCTGTGGCCTGAGTGGGTGGTGGCAGAGAGAAGCCGAGGCTTGGGGCTCTTGGGGACCCCTGGTGG
AAATGAAATGTGCTGGGACTTGTTGATGCTCTCTTTCACCAAATGCTGGGGATGCAGCAGGGAGCCAAACAGACAATTCT
GCCTTGTGGAGCTTTTCCATCTCAGGGGAAGCTGACAGCAAACAAGTGAAGATTTCTGGCCTGGGGCcaggcggggggga
ggggcgggtggGCGAAAGCAGGGAGTCAGGGATGAGAGAGGAGAAGGGCTGGGAGTGGGTTTGAGGCTTTAGAGAGGCTG
AGTGGGAGAGCAAACACCTGGGGAGAGAGGTTTGCAAGCTGAGAAGCCAGCTGGCTGgtgaagggatggagggagagagg
agacaatgtaggggcggggaggggggggtgcaGATTTTATAGGGCCTCGCGGGCCATTTGGGGAGCCGTGAGCAGGTGtt
tatatttacatgttttgatatttttatccTCCTGTTTGTATTTGACATGCAcgttccttttactttttaaaccactttgt
tgagttataattgacattCAACACATTTAAACATCACACATTTAAAGCCTGCAGTTTGACATTTTGACTTCTGTGTATAC
CTGTGAAACCAGGACCACAAACGAGAGTGTGAGCACACCCGTCTCGCCCCAGGCGCCTCTGTGGCCTCTCCCTTCCGCTC
CTTCTGCCTCCCATTTCTAAGCAACTGCCGCTCTGTTTTCTGTCACCAGACACAAGTGTACATTTTGTGGACTTTTGTGT
AAATGGAATTACACAGTGGGTGTGCTTTCTTGGCCTGGCCTCTGCCGGTGTCATTGCTGTGAGTTCCATCTCGGTCACTA
CACGTGTCCATAGCTCATTCCTGTTTAATGCTGACGAACCTTCCAGTGTATGGATGTGTCCCAGTTTGTGTGTTCACCTA
TTGGTGAacttttggattatttctatgttttctttttttgttttttgtttttttactttatttagttatttgataGAGGC
AGTGgggagcatgagccaggggaggagcagagggagaagcagactccccactgaacagggagcccgacgccaggcttgat
cccaggaccccaggatcatgacctgagctgaagacagatgcttaatggaccGAGCCACTGTATGTTTTGCTTttgattga
aatataaaattcacgTGGAGAAATGCTGGTATCACAAGTGTGCAGATCAGTGTGTTGCcctcagatcaagaaatagatCT
CCCCCCCAGGACTCTAGAAACCCCTAGTGTGTTCCCTCCCTATCTCACTGTTACTACCACCCAGACTTCTGTTAGCGCAG
AGCAGTTCTGCTTGCCCTCCTATTCCATGAACTCACAAATGtcctatgtgtgtgtctcatccGTGTTCTAAGTGTAAGTC
GTACACTGTTTATCGGTCCTGCCGTTGAAGGGCCTCTGGGAGCTGCCAGCTGGGGCCACTAGGAACAGTGCTGCCCTATG
AATATTCTGGTGCGTGTCTTTGGTGGACATGCATGCACctccctgctgggccctgggggttgCATGTGTCAACCTGAGTA
CGTACTGCCCTGTGGTTCGCCAGAGCCATGTGCTCACGTACACTGCCCCCTGCACAGCCACAGATAGAAGtcctgctgct
ccacatcctcgcTGATGCTTTGTGTTTTCCGTCTTCTCCATCCGGGCGGGTACACAATGGCCTCTTGTACTTTTCATTTG
CGCTTCCCCCGGAAGAGTTCTGACTCGAGTCGGGCTGTGTTGGGATGGCCCCAGCTCACGCTCCCTCGTCCCTGTCTCTT
TCAGGCCGGGTCCTTGTCCACTGCCGGGAAGGTTACAGCCGCTCCCCAACCCTAGTTATCGCGTACCTCATGATGCGGCA
GAAGATGGATGTCAAGTCTGCCCTGAGCATCGTGAGGCAGAACCGTGAGATCGGCCCCAACGATGGTTTCCTGGCCCAGC
TATGCCAGCTCAATGACAAACTAGTCAAGGAGGGGAAATTGAAACTCTAGGGCACTCCCGCTGCCTCTTCTCTAGCGGCA
GACAGGGGAGGCCCTGGT
1 change: 1 addition & 0 deletions test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa.fai
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chr9 8978 29 80 81
11 changes: 11 additions & 0 deletions test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff
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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
chr9 ensembl mRNA 100 8978 . + . ID=transcript:ENSCAFT00000047742;Parent=gene:ENSCAFG00000028570;Name=DUSP3-201;biotype=protein_coding;transcript_id=ENSCAFT00000047742;version=2
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
chr9 ensembl CDS 100 104 . + 0 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
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
chr9 ensembl CDS 106 225 . + 1 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
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
chr9 ensembl CDS 2976 3202 . + 1 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
chr9 ensembl CDS 8725 8930 . + 2 ID=CDS:ENSCAFP00000041069;Parent=transcript:ENSCAFT00000047742;protein_id=ENSCAFP00000041069
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
chr9 ensembl three_prime_UTR 8931 8978 . + . Parent=transcript:ENSCAFT00000047742
3 changes: 3 additions & 0 deletions test/csq/ENSCAFT00000047742/test.txt
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104 CA C synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
104 CA C synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding

7 changes: 7 additions & 0 deletions test/csq/ENSCAFT00000047742/test.vcf
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##fileformat=VCFv4.2
##contig=<ID=chr9,length=249250621>
##INFO=<ID=type,Number=.,Type=String,Description="">
##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
##INFO=<ID=EXPL,Number=1,Type=String,Description="Expected consequence with bt/csq -l">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr9 104 . CA C . PASS EXP=synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding

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