From 3851fbd5670cc45b6bd8026be65fd7714442db09 Mon Sep 17 00:00:00 2001 From: Andrew Whitwham Date: Mon, 30 Sep 2024 15:07:46 +0100 Subject: [PATCH] Second attempt to enable indexing from vcf. First attempt tried to avoid an internal bcf conversion in order to maintain speed. This version does uses the conversion code already in place to make the indexing easier. --- vcfconcat.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vcfconcat.c b/vcfconcat.c index 232b3ae3..d2cf7282 100644 --- a/vcfconcat.c +++ b/vcfconcat.c @@ -641,7 +641,7 @@ static void concat(args_t *args) bcf_hdr_remove(hdr, BCF_HL_FMT, NULL); bcf_hdr_destroy(hdr_ori); } - if ( !fp->is_bin && args->output_type&FT_VCF ) + if ( !fp->is_bin && args->output_type&FT_VCF && !args->out_fh->idx) { line->max_unpack = BCF_UN_STR; // if VCF is on both input and output, avoid VCF to BCF conversion