From 88341056971a46013deccbbad40869291a524094 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 31 Jan 2024 13:07:48 +0100
Subject: [PATCH] fix argument issues

---
 src/bgzip/config.vsh.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml
index 159c33e8..6a5e7f49 100644
--- a/src/bgzip/config.vsh.yaml
+++ b/src/bgzip/config.vsh.yaml
@@ -30,7 +30,7 @@ functionality:
         description: name of BGZF index file [file.gz.gzi]
     - name: Arguments
       arguments:
-      - name: offset
+      - name: --offset
         alternatives: -b
         type: integer
         description: decompress at virtual file pointer (0-based uncompressed offset)
@@ -79,6 +79,7 @@ functionality:
         [[ "$par_binary" == "false" ]] && unset par_binary
         bgzip -c \
           ${meta_cpus:+--threads "${meta_cpus}"} \
+          ${par_offset:+-b "${par_offset}"} \
           ${par_decompress:+-d} \
           ${par_rebgzip:+-g} \
           ${par_index:+-i} \
@@ -87,6 +88,7 @@ functionality:
           ${par_reindex:+-r} \
           ${par_size:+-s "${par_size}"} \
           ${par_test:+-t} \
+          ${par_binary:+--binary} \
           "$par_input" > "$par_output"
   test_resources:
     - type: bash_script