From 863a213bfb75c7144ea5b6c32b6490f27139f41e Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 5 Jul 2021 15:53:31 +0200
Subject: [PATCH 1/2] removing creating old symlinks for concordance check

---
 bin/copyProjectDataToPrm.sh | 28 ----------------------------
 bin/processGsRawData.sh     |  2 +-
 2 files changed, 1 insertion(+), 29 deletions(-)

diff --git a/bin/copyProjectDataToPrm.sh b/bin/copyProjectDataToPrm.sh
index cdc57211..6bbc80c4 100755
--- a/bin/copyProjectDataToPrm.sh
+++ b/bin/copyProjectDataToPrm.sh
@@ -196,34 +196,6 @@ function rsyncProjectRun() {
 			cd "${PRM_ROOT_DIR}/projects/${_project}/"
 			if md5sum -c "${_run}.md5" > "${_run}.md5.log" 2>&1
 			then
-				cd "${PRM_ROOT_DIR}/concordance/${PRMRAWDATA}/"
-				mapfile -t files < <(find "${PRM_ROOT_DIR}/projects/${_project}/${_run}/results/${CONCORDANCEFILESPATH}" -mindepth 1 -maxdepth 1 \( -type l -o -type f \) -name "*.${CONCORDANCEFILESEXTENSION}")
-				for i in "${files[@]}"
-				do
-					if [[ "${_sampleType}" == 'GAP' ]]
-					then
-						local _belowSDThreshold="False"
-						_belowSDThreshold="$(awk '{if ($1 <0.2){print "True"}else {print "False"}}' "${i}.sd")"
-						if [[ "${_belowSDThreshold}" == 'True' ]]
-						then
-							ln -sf "${i}" .
-						else
-							log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "SD for ${i} is higher than 0.2; skipped"
-						fi
-					else
-						log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "Making symlinks for concordance check."
-						ln -sf "${i}" .
-						# shellcheck disable=SC2153
-						log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "Navigating to /groups/${GROUP}/${COMP_PRM_LFS}/concordance/${PRMRAWDATA}/ to create symlink for concordance check on the complementary prm"
-						cd "/groups/${GROUP}/${COMP_PRM_LFS}/concordance/${PRMRAWDATA}/"
-						ln -sf "${i}" .
-						log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "navigating back to ${PRM_ROOT_DIR}/concordance/${PRMRAWDATA}/ to create symlink for original prm"
-						cd - 
-					fi
-				done
-				log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "Removing symlink for project VCF."
-				rm -f "${PRM_ROOT_DIR}/concordance/${PRMRAWDATA}/${_project}.final.vcf.gz"
-				cd "${PRM_ROOT_DIR}/projects/${_project}/"
 				if [[ "${_sampleType}" == 'GAP' ]]
 				then
 					log4Bash 'DEBUG' "${LINENO}" "${FUNCNAME:-main}" '0' "_sampleType is GAF. Making symlinks for DiagnosticOutput folder."
diff --git a/bin/processGsRawData.sh b/bin/processGsRawData.sh
index 8c9753e2..ceb69022 100755
--- a/bin/processGsRawData.sh
+++ b/bin/processGsRawData.sh
@@ -901,7 +901,7 @@ else
 		#
 		if [[ -e "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished" ]]
 		then
-			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished present -> Data transfer completed; let's process batch ${gsBatch}..."
+			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "exit present -> Data transfer completed; let's process batch ${gsBatch}..."
 			sanityChecking "${gsBatch}" "${controlFileBase}"
 		else
 			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished absent -> Data transfer not yet completed; skipping batch ${gsBatch}."

From 07634b525f7382393415d14af2cb22424d4962d5 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 5 Jul 2021 16:43:21 +0200
Subject: [PATCH 2/2] undo change

---
 bin/processGsRawData.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/processGsRawData.sh b/bin/processGsRawData.sh
index ceb69022..8c9753e2 100755
--- a/bin/processGsRawData.sh
+++ b/bin/processGsRawData.sh
@@ -901,7 +901,7 @@ else
 		#
 		if [[ -e "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished" ]]
 		then
-			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "exit present -> Data transfer completed; let's process batch ${gsBatch}..."
+			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished present -> Data transfer completed; let's process batch ${gsBatch}..."
 			sanityChecking "${gsBatch}" "${controlFileBase}"
 		else
 			log4Bash 'TRACE' "${LINENO}" "${FUNCNAME[0]:-main}" '0' "${TMP_ROOT_DIR}/${gsBatch}/${gsBatch}.finished absent -> Data transfer not yet completed; skipping batch ${gsBatch}."