segfault +setGT -i'INFO/DP' #982
Description
I'm trying to set positions with total depth of less than 2 as missing using setGT:
bcftools +setGT -O v -o test.out in.vcf.gz -- -n . -t q -i'INFO/DP<2'
Segmentation fault
Whereas
bcftools +setGT -O v -o test.out in.vcf.gz -- -n . -t q -i'FORMAT/DP<2'
Filled 132 alleles
header lines:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##source=ATLAS
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods">
##FORMAT=<ID=GG,Number=10,Type=Integer,Description="Phred-scaled likelihoods for all genotypes in alphabetical order">
##contig=<ID=1>
##contig=<ID=2>
##contig=<ID=3>
##contig=<ID=4>
##contig=<ID=5>
##contig=<ID=6>
##contig=<ID=7>
##contig=<ID=8>
##contig=<ID=9>
##contig=<ID=10>
##contig=<ID=11>
##contig=<ID=12>
##contig=<ID=13>
##contig=<ID=14>
##contig=<ID=15>
##contig=<ID=16>
##contig=<ID=17>
##contig=<ID=18>
##contig=<ID=19>
##contig=<ID=20>
##contig=<ID=21>
##contig=<ID=22>
##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">
##bcftools_viewVersion=1.9+htslib-1.9
Info lines:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Molz1
1 752566 . G A . . DP=16;AC=2;AN=2 GT:AD:DP:GQ:PL:GG 1/1:0,16:16:48:472,48,0:0,48,48,48,616,511,616,472,511,616
if I run:
bcftools view -i'INFO/DP<2' in.vcf.gz > test.out
I get the correct output, suggesting there is something up with the plugin?