fix gvcf issue

Author: JasonCLEI

scripts/clair3.sh

@@ -188,7 +188,6 @@ ${PYPY} ${CLAIR3} SortVcf \
     --cmd_fn ${OUTPUT_FOLDER}/tmp/CMD \
     --ref_fn ${REFERENCE_FILE_PATH} \
     --pileup_only ${PILEUP_ONLY} \
-    --output_all_contigs_in_gvcf_header ${OUTPUT_ALL_CONTIGS} \
     --print_ref_calls ${SHOW_REF} \
     --haploid_precise ${HAP_PRE} \
     --haploid_sensitive ${HAP_SEN} \
@@ -362,6 +361,7 @@ then
         --input_dir ${TMP_FILE_PATH}/merge_output \
         --vcf_fn_prefix "merge" \
         --vcf_fn_suffix ".gvcf" \
+        --output_all_contigs_in_gvcf_header ${OUTPUT_ALL_CONTIGS} \
         --output_fn ${OUTPUT_FOLDER}/merge_output.gvcf \
         --sampleName ${SAMPLE} \
         --ref_fn ${REFERENCE_FILE_PATH} \
@@ -438,4 +438,4 @@ echo $''
 echo "[INFO] Finish calling, output file: ${OUTPUT_FOLDER}/merge_output.vcf.gz"
 
 if [ ${FINAL_WH_PHASING} == True ]; then echo "[INFO] Finish calling, phased output file: ${OUTPUT_FOLDER}/phased_merge_output.vcf.gz"; fi
-if [ ${FINAL_WH_HAPLOTAG} == True ]; then echo "[INFO] Finish calling, phased output BAM file: ${OUTPUT_FOLDER}/phased_output.bam"; fi
+if [ ${FINAL_WH_HAPLOTAG} == True ]; then echo "[INFO] Finish calling, phased output BAM file: ${OUTPUT_FOLDER}/phased_output.bam"; fi