From e660954c0e3f441dc5b8c6ccfaa79caeea5079d5 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Tue, 23 Jan 2024 09:22:12 -0600
Subject: [PATCH] put the input in the correct place

---
 pggb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pggb b/pggb
index edb0f93..ec6c9c7 100755
--- a/pggb
+++ b/pggb
@@ -669,7 +669,7 @@ if [[ $vcf_spec != false ]]; then
 
             #TODO: remove "bcftools annotate" when vcfwave will be bug-free.
             # The TYPE info sometimes is wrong/missing and there are variants without the ALT allele.
-            bcftools sort -T "$temp_dir" | bcftools annotate -x INFO/TYPE "$vcf_decomposed_tmp"  | awk '$5 != "."' > "$vcf_decomposed"
+            bcftools sort -T "$temp_dir" "$vcf_decomposed_tmp" | bcftools annotate -x INFO/TYPE | awk '$5 != "."' > "$vcf_decomposed"
             rm "$vcf_decomposed_tmp" "$vcf".gz
 
             bcftools stats "$vcf_decomposed" > "$vcf_decomposed".stats