vcfwave generates VCF files with invalid rows

[AndreaGuarracino]

Given this pipeline:

fin=scerevisiae8.fa.gz.a9c917e.e34d4cd.d31edad.smooth.final.SGDref.haplo.vcf.gz
fout=scerevisiae8.fa.gz.a9c917e.e34d4cd.d31edad.smooth.final.SGDref.haplo.waved.vcf.gz

vcfbub -l 0 -a 100000 --input $fin | vcfwave -I 1000 -t 16 | bgzip -c -@ 16 > $fout

The output presents invalid rows:

• the TYPE field sometimes is wrong and incomplete

zgrep 987945 $fout

SGDref#1#chrIV	987945	>420266>421972_55	TATGTCATATTGAATTTCCTCATCACTTTCGCCTAGATTTATAATCTTGGTGTCGTATTGCATCTTAAGCTTCTCTATAATTCTTTTGTTTGAATTTAGATTTTTGCTAAACAATACCATATCATCTACGAATAAACAAATTGTCACTTGAC	AATGTCATATTGAATTTCCTCATCACTTTCGCCTAGATTTATAATCTTGGTGTCGTATTGCATCTTAAGCTTCTCTATAATTCTTTTGTTTGAATTTAGATTTTTGCTAAACAATACCATATCATCTACGAATAAACAAATTGTCACTTGAC,TATGTCGTACTGAATTTCGTTATCACTTTCACCCAGATTTATTATCTTTGTATCGTATTGTTTCTTGAGTGTTGTTATGATTTTCTTATTTGCATTTAAGTCTTTGCTGAACAATATCATATCATCAACGAATAAGCAAATTGTTACTTGAC	60	.	48=SGDref#1#chrIV:981143,SGDref#1#chrIV:981143;AC=1,2;AF=0.142857,0.285714;INV=1,1;LEN=1,0;TYPE=snp,	GT	2	.	0	2	.	1	.

• the ALT allele sometimes is missing

zgrep SGDref#1#chrMT $fout | grep 9878

SGDref#1#chrMT	9878	>627557>627676_51	A		60	.	48=SGDref#1#chrMT:9296;AC=1;AF=0.142857;INV=0;LEN=1;TYPE=complex	GT	0	0	0	0	0	1	0

scerevisiae8.fa.gz.a9c917e.e34d4cd.d31edad.smooth.final.SGDref.haplo.vcf.gz
scerevisiae8.fa.gz.a9c917e.e34d4cd.d31edad.smooth.final.SGDref.haplo.waved.vcf.gz

[pjotrp]

The new vcfwave code on trunk (--nextgen switch) should not have these issues because it does not try to have multiple alleles on one line and is a lot cleaner: https://github.com/pjotrp/vcflib/blob/master/src/vcfwave.cpp#L240. I'll make a release in the coming days after more testing.

[pjotrp]

@AndreaGuarracino can you confirm this is fixed?