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Plugin allele-length causes segmentation fault for alleles larger than 500 #1837

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pontushojer opened this issue Dec 13, 2022 · 1 comment
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Plugin allele-length causes segmentation fault for alleles larger than 500 #1837

pontushojer opened this issue Dec 13, 2022 · 1 comment

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@pontushojer
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This is the output I got when running bcftools +allele-length.

bcftools +allele-length Peregrine_HiFi_asm3bc.vcf.gz
Segmentation fault: 11

After some digging I finally narrowed it down to this entry in the VCF causing the issue

chr1	729578	.	AGTTCAGGGCCTGGAGAGAAGGCTGGGAGGCAGGAGCTGGGTCTAAAGAGGCCATTGTAACGATGGAGCTGTGCCTGTGGAGGCTGTTGTGAGGCAGTAGCCTCATCTGCGGAGGCTGCCGTGACATAGGGTATGGGCCTAAATAGGCCATTGTGAGTCATGAGCTTGGTCTGTAGAGGCTGACTGGAGAAAGTTCTGGGCCTGGAGAGGCTGCCGGGAGGTAGGAGCTGGGCCAAAAGATGTAAGCACATTTGCATTTATTAGGCACTTTATTTCCATTATTACACTGTAATATATAATAAAATAATTATAGAACTCACCATAATGTAGAATTAGTGGGCGTGTTAAGCTTGTTTTCCTGCAACTGAATGGTCCCACCTGAGCGTGATGGGAGAAAGTGACAGATCAATAGGTATTAGATTCTCATAAGGACAGCGCAACCTCGATCCCTCACATGCACGGTTCACAACAGGGTGCGTTCTCCTATGAGCATCTAATGCTGCTGCTCATCTGAGAAGGTGGAGCTCAGGTGGGAATGTGAGCAAAGGGGAGTGGCTCTAAATACAGACGAAGCTTCCCTCACTCCCTCACTCGACACCGCTCACCTCCTGCTGTGTGGCTCCTTGCGGCTCCATGGCTCAGGGGTTGGGGACCCCTGCTCAAGTGCATCCAAAGCGACCCTTCCCACACCAGTCTTCACAGTGGTCAAGGGCAGCAACCACTTAGCTCCCAAGGCATGTGCCTCAGCTGGCATTTCGTCACAATCAACAGTAAGTGGTAGCTTGAGTCACTGTGAGGTCACCTACTGGAAATCACCAGCACCCCATTTCCCACTGGCAAAGAGCTCAGCACTGCCCCCTGGGAAACCAAACCTATGCCCAAATCCCATCTGTGTGGGTCTACCTCCTGGGACCCTTCCTAACATATTAGTCAGAGTCCAATCAGGAAGCATAAACCACTCAAAAGTTTAAAGTGGTAAAATTTAATACAGAGAATTATTCATTATAACAGGTGAACAGCATAATGAGAGATTGGCTAGCACAGAGTAAAGAGAACTCTAGAGAATATGGGACTAGCCCAGGCCAGGCATGGTGGCTCATGCCTGAAATTCCAGCCATTACAGAAGCTAATGCAGGAGGATTGCTTAAGGCCAGGAGCTAGAGACCGGTCTGGACGACACAGTGAGACCCTGTCTCTATCCAAAAGAAGAAAAAAGTTAGCTGGGGGTGGTGGTGCACACTTGTAGTCCCAGCTACTCAGAATGCTGAAGTTTGAGCCTGGGAGGTCAAGGCTGCAGTGAGGCATGATTATGCCACTACAGTCCAGCCGGATGACAGAGCAAGACCCTGTCTCAAAGAACAAAACCACAACAACCATTTACAGACAGAAAAGAAATAGAGCTAATAAGCTGAGGAAAGATGTTGAAATGTGACAAGTAAAGTAATATGAGGTCTTTTGTCTATTTAAAATAATCAAACAAAAAATGGCTTACGAAATTATAATACCCTGTGCTGGCAAAGGTGCAGTGAAATGGGCACTTTCTTATACTATGAGGGGTGGTTAAATTGTGTATAAGCCTTCCAGGGTAAAGCCTGTCAATTTTTTAAAATAATGGAGACAGGGTCTCACCATACTGCCATACTGCCTCCTCCAACTCTTGGCCTCAAGCAATCCTCCTCTCTTAGCCTCCCAAAGTGCTAAGATTATAGCTGGGAGGCACCCAAAACCCTGTCAATTTACATCAAGGGTAAGGAGAATGTCCATTCACCATGACTCACAGTAATCTTACTTCTGGGGAGACAATTCAATCTAAGCAAAAGGTCATCTGTACACACACAGTAAAAATCTGGGAGTAACTGAAGACAGAGTTGGTAAGTGAAATAAGAAACAGTTATAAGAAATTAAACTATGGTATCAATAGGCACCTGGTAAAAGGTCAGTTGATGTTAGCTGCTACTTTTTTGTTGTTTTGAGACAGGGTCTCACTCTGTCACCCAGGCTGGAGTGCAGAGGCCTGATCATGACTCACTGCAGTCTCAGCCTCCCTGGGCTCAAGTGATCCTCCCACCTCAGCCTCCCAAGTAGCTGGGACTACAGGAACATGCCACCACACTAGGCTAATTCATGTATTTTTCTGTAGGGATGGTGACTCCCCCTTTGTTTCCAAGGCCTATCGCAAACTCTTGGCCTCGAGCCATCCTCCTGCCTCAGCCTCCCAAAGTGTTGTGATTACCAGTGTGAGCCACCACACCTGGCCAGCTGCTACTTTTATCAATATTATTCTTATTCCACTCAATTAAAAATTATTATTTTCAAGGCTATGCAACAGTATGTATCCTACAGCGTAATTGTAAAAACATACACAGTCGTCATCCCTCAGTATACAGAATTAGTTCCAGCCCCCCATCTCTGCATATACCAAAATCCATGCTTACTCACGTTTCGCTGTCACCCCTCTAGAATCCACGTATACGAAAATTCCAAATGTTAGTTGGGCATAGTGGCAAGCACCTGTAGTCTCAGCCACGTGGGAGGTTGAGGTGGGAGGATCGCTTCAGCCTGGAAGGTTGAGGCTGCAGTCAGCTGCGATAGCACTACTACACTCCAGCCTTGGACAACAGAGGGAGACCCTGTCTCAGAAAAAAAAACAAAATAAAACAGGTTAGAAATTGTAATGAGGTCTGCTGGGCAAAATTCCATATAAGCAATGTATAAATTAATAAAGCAAATCGTGATAAATTAGTACGATTGACTTTCTGGAGTTTCTGACAATAAAAGTAAGGAAAATGCAGAACACAAAGACAGAGAGTAAAAAGAGAAATTAGGAAAGCATTCTACATGTTGAATAGGAAGACACTGGCCATGTTCGTGCAGCGGCAGTATGTCGTGACATGACATACCTTGGAGAGAAGTTAACAGATGAGGAAGTTGATAAAAATCATCAGAGAAGCAAAATACTGGTAGCGACACTCAAGTAAACCATGAAATTTCCATAACTTATGTCAGCAAAGTGGGAATATTGTACAGTGTGTGTTGAAGTTCCTATACAACATTGTTTATCTGCCTTTTGTTTGTTTGTAAGGAATGTACATACTAAAAGTTCTTCTTGCTGTCAAAAGAATATGCGTGAATAAGTCATTTTAACTTATTCTTCTGTTTTTCTTTTATCTTCCTGCCATCATCCCACAGCCTTACTTTAGAAATTTCTTTTTTAGAAAATTGAACAAGTGCTCCCTGTGGTGGCACATACCTCGAGGATGGGAGGCAGGGGTGGAAGGGTCACTTGAGGCCATTAGTTTGACACCAGCCTGGCCAACAAAGTGAGACCCCGTGTCTACAAAACAATTTAAAAATTAGCCAAGTATCGTCATGTATACCTACAGTCCCAGCTATCTGAACTTACTGAGAAT	A	30	.	.	GT:AD	0|1:1,1

This is quite long at 3410 bp. Looking at the source code I then found that the length is currently capped at 512.

bcftools/plugins/allele-length.c

Line 30 in d80a35f

#define MAXLEN 512

Its not so helpful to only get a seg-fault here. Two solutions would be:

  • Raise some kind of warning that there are alleles longer than 512 bp.
  • Aggregate alleles larger than 512 bp as final line in the output.
@pd3 pd3 closed this as completed in c380ab0 Jan 4, 2023
@pd3
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pd3 commented Jan 4, 2023

Fixed according to your second suggestion. Thanks for the bug report

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@pd3 @pontushojer