Merge pull request #384 from pangenome/fix_vg_deconstruct_sep

explicit separator for vg 1.40.0
pangenome · Apr 1, 2024 · 4955406 · 4955406
2 parents 7bb5b78 + 59c0f73
commit 4955406
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/pggb b/pggb
@@ -670,7 +670,7 @@ if [[ $vcf_spec != false ]]; then
         if [[ ! -s $vcf || $resume == false ]]; then
           echo "[vg::deconstruct] making VCF with reference=$ref and delim=# xxxxxxxxxxxxx $s ------------ $pop_length"
           ( TEMPDIR=$(pwd) $timer -f "$fmt" vg deconstruct -P "$ref" \
-                   -e -a -t $threads "$prefix_smoothed_output".final.gfa >"$vcf" ) 2> >(tee -a "$log_file")
+                   -H "#" -e -a -t $threads "$prefix_smoothed_output".final.gfa >"$vcf" ) 2> >(tee -a "$log_file")
           bcftools stats "$vcf" > "$vcf".stats
         fi