From b87d9d82fde81d6ba923adb0dd53175d57f7ab11 Mon Sep 17 00:00:00 2001
From: zhengzhenxian <920596906@qq.com>
Date: Thu, 19 May 2022 21:15:32 +0800
Subject: [PATCH] skip full-alignment calling when no candidate was selected

---
 scripts/clair3.sh        | 1 +
 scripts/clair3_c_impl.sh | 1 +
 2 files changed, 2 insertions(+)

diff --git a/scripts/clair3.sh b/scripts/clair3.sh
index 0f7fe4d..32c2651 100755
--- a/scripts/clair3.sh
+++ b/scripts/clair3.sh
@@ -254,6 +254,7 @@ time ${PARALLEL} --retries ${RETRIES} --joblog ${LOG_PATH}/parallel_5_select_can
 
 echo $''
 echo "[INFO] 6/7 Call low-quality variants using full-alignment model"
+if [ "$( ls ${CANDIDATE_BED_PATH}/FULL_ALN_FILE_* | wc -l )" -eq 0 ]; then echo "[INFO] No Candidate found! Exit in selecting full-alignment candidates"; exit 0; fi
 cat ${CANDIDATE_BED_PATH}/FULL_ALN_FILE_* > ${CANDIDATE_BED_PATH}/FULL_ALN_FILES
 time ${PARALLEL} --retries ${RETRIES} --joblog ${LOG_PATH}/parallel_6_call_var_bam_full_alignment.log -j ${THREADS_LOW} \
 "${PYTHON} ${CLAIR3} CallVarBam \
diff --git a/scripts/clair3_c_impl.sh b/scripts/clair3_c_impl.sh
index bee42f7..af83d57 100755
--- a/scripts/clair3_c_impl.sh
+++ b/scripts/clair3_c_impl.sh
@@ -241,6 +241,7 @@ time ${PARALLEL} --retries ${RETRIES} --joblog ${LOG_PATH}/parallel_5_select_can
 
 echo $''
 echo "[INFO] 6/7 Call low-quality variants using full-alignment model"
+if [ "$( ls ${CANDIDATE_BED_PATH}/FULL_ALN_FILE_* | wc -l )" -eq 0 ]; then echo "[INFO] No Candidate found! Exit in selecting full-alignment candidates"; exit 0; fi
 cat ${CANDIDATE_BED_PATH}/FULL_ALN_FILE_* > ${CANDIDATE_BED_PATH}/FULL_ALN_FILES
 time ${PARALLEL} --retries ${RETRIES} --joblog ${LOG_PATH}/parallel_6_call_var_bam_full_alignment.log -j ${THREADS_LOW} \
 "${PYTHON} ${CLAIR3} CallVariantsFromCffi \