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The -t, --targets option misses first record of new sequence #1441

@pd3

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@pd3

This command

echo -e "##fileformat=VCFv4.2\n##contig=<ID=1,length=248956422>\n##contig=<ID=2,length=248956422>\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n1\t1\t.\tA\tC\t.\t.\t.\n2\t1\t.\tA\tC\t.\t.\t.\n2\t2\t.\tA\tC\t.\t.\t." | bcftools view -Ht 2

outputs

2	2	.	A	C	.	.	.

but should output

2	1	.	A	C	.	.	.
2	2	.	A	C	.	.	.

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htslib-dependentCannot be fixed until htslib is fixed

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