Lack of variation causes segfault in polyphase

[jan-glx]

Whatshap polyphase segfaults if a chromosome contains no variants but none of them are phased (or something like that).
reproducible example (Same data, reference and locus as in #493, different vcf file)

wget https://hgdownload.cse.ucsc.edu/goldenpath/mm10/chromosomes/chr19.fa.gz && gunzip chr19.fa.gz
samtools faidx chr19.fa
bind 'set disable-completion on'
cat <<'EOF' > unphased_freebayes.vcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele not already represented at this location by REF and ALT">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##contig=<ID=chr19,length=61431566>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CGAAGAGGTAGGTGCGAG-1
chr19	55910646	.	ACAAATCCCCCATC	AAATC,ACAAATCCC	1486.28	.	AC=1,1	GT:DP:AD	1/2:83:0,35,44
EOF

cat <<'EOF' > reads.sam
@HD	VN:1.4	SO:coordinate
@SQ	SN:chr19	LN:61431566
@RG	ID:CGAAGAGGTAGGTGCGAG-1	SM:CGAAGAGGTAGGTGCGAG-1
@PG	ID:bwa	VN:0.7.12-r1039	CL:bwa mem -C -M -t 32 -H .sam.header .fa .fastq.gz .fastq.gz	PN:bwa
A01382:376:H5HVGDRX3:1:2131:30807:22842	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTCTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C54T39	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:11	MQ:i:60	AS:i:135	XS:i:19
A01382:376:H5HVGDRX3:1:2252:12048:7200	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:1:2264:23258:10457	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFF,FFFFFFFFFFFFFF:FFFFFFF:FFFF:FFF:,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFFFFFF,FFF:F:FF:FFFFFF:FFFFF:F:,:FF,FFFF:FFFFFFF:FFFFFF:FFFF,FFFFFFFF:FFF,FFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:2:2105:19253:5024	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGCACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFF:F:FFF::FFFFFFFFFFFFFFF:FFF:FFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C18T75	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:11	MQ:i:60	AS:i:135	XS:i:19
A01382:376:H5HVGDRX3:2:2105:19271:5431	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGCACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C18T75	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:11	MQ:i:60	AS:i:135	XS:i:19
A01382:376:H5HVGDRX3:2:2167:16938:3302	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGACATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTGGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FF:FFFFF,F:FFFFFFFFFFF::FF:FFFFFFF,F,,FFFFFFFFFFFFFFFF,FF:FFFF,FFFFF:FFFFFFFFFFF:FFF,FF:FFFFFFFFFF:FFFFFFFF:::FFFFFFFF:FFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF	MC:Z:109M	MD:Z:25T35A3^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:12	MQ:i:60	AS:i:130	XS:i:20
A01382:376:H5HVGDRX3:2:2231:9245:11741	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:2:2236:29125:20431	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFF,F,F:,FFFFFFF:FFFFFFF:F:FFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,:,:FFFFFFFFF:FFFFFFFFFFFFFFF:FFFF::FFFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:2:2259:3025:9549	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:2:2274:11460:6934	147	chr19	55910582	60	65M9D95M	=	55910535	-216	TCCCAAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGAAATCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF	MC:Z:109M	MD:Z:65^CAAATCCCC0C94	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:10	MQ:i:60	AS:i:140	XS:i:20
A01382:376:H5HVGDRX3:1:2247:22309:12164	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:5	MQ:i:60	AS:i:149	XS:i:20
A01382:376:H5HVGDRX3:2:2137:18249:27336	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF:F:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,F:FFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:5	MQ:i:60	AS:i:149	XS:i:20
A01382:376:H5HVGDRX3:2:2206:5638:6026	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:,,F:FF:F,FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:5	MQ:i:60	AS:i:149	XS:i:20
A01382:376:H5HVGDRX3:2:2227:24740:17628	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF::F,FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F,FFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:5	MQ:i:60	AS:i:149	XS:i:20
A01382:376:H5HVGDRX3:2:2252:15700:25144	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:5	MQ:i:60	AS:i:149	XS:i:20
A01382:376:H5HVGDRX3:2:2255:32018:34898	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAACCCCCGCTAGGATGGTTGGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	,:FFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:F,:FFFF:FF	MC:Z:109M	MD:Z:65T2^CCCAT14A77	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:7	MQ:i:60	AS:i:139	XS:i:19
A01382:376:H5HVGDRX3:2:2270:19180:5181	147	chr19	55910586	60	68M5D92M	=	55910535	-216	AAGGCCTCCGCACCCTCCAGATATCTCTCCATATTACCCGCTGTCGCCCGGCACCGTAGGACAAATCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTCTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	FF,FFFFF:FFFFFFFFFFFF,FF:FFFFFFF:F,FFFFFFFFFFFFFFF:FFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFF:FFFFFFFFFFFFFFFF:FF,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	MC:Z:109M	MD:Z:68^CCCAT56T35	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:6	MQ:i:60	AS:i:144	XS:i:19
A01382:376:H5HVGDRX3:1:2145:13051:6527	147	chr19	55910620	60	34S34M5D92M	=	55910535	-216	CCCGCCCCCCCACCCACCAGATCTCTCGCCACACTACCCGCCGTCGCCCGGCACCGTAGGACAACTCCCCGCTAGGATGGTTAGTACCACAGTAAGCAATTCCAGTTTTTAATTCCCTTTTTGTTTCTTGCATGAGCATGCTTATTAGTTTACGTGTACG	:,,,FF,FF,F,FFF,FFF,:,,,F,F,FF,,,,,FFFFFF,F:F:FFFFFF:FFF:FF:FF:F,FFFFF,FFFF,:FF:F:FF,FFFF:FF,F:F:FF:FFFFFFFF:F,::FFF::FF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFF	MC:Z:109M	MD:Z:7T22A3^CCCAT92	RG:Z:CGAAGAGGTAGGTGCGAG-1	NM:i:7	MQ:i:60	AS:i:105	XS:i:20
EOF

bind 'set disable-completion off'

samtools view reads.sam -b > reads.bam
samtools index reads.bam

whatshap --debug polyphase --ploidy 2 --reference=chr19.fa unphased_freebayes.vcf reads.bam

output

This is WhatsHap (polyploid) 2.1 running under Python 3.12.0
DEBUG: Read groups in CRAM/BAM header: [{'ID': 'CGAAGAGGTAGGTGCGAG-1', 'SM': 'CGAAGAGGTAGGTGCGAG-1'}]
DEBUG: Reading the input VCF to find possibly missing headers
DEBUG: Missing contigs: []
DEBUG: Missing formats: ['AD']
DEBUG: Missing infos: []
DEBUG: Found 1 sample(s) in the VCF file.
DEBUG: Parsed 0 SNVs and 1 non-SNVs. Also found 1 multi-ALTs.
======== Working on chromosome 'chr19'
---- Processing individual CGAAGAGGTAGGTGCGAG-1
Number of variants skipped due to missing genotypes: 0
Number of remaining heterozygous variants: 1
DEBUG: Reading alignments for sample 'CGAAGAGGTAGGTGCGAG-1' on chromosome chr19 and detecting alleles ...
Found 7 reads covering 1 variants
Kept 0 reads that cover at least two variants each
Segmentation fault

I am using 07129fd . See also #441, which seems to be the same issue but has been resolved?

[marcelm]

The fix in #441 was apparently never merged. I’ve opened #497.

[schrins]

Oh, that was my fault. I will likely not have time to fix it today, but at some time over the weekend.