From b410689019a09e58a9f5e065f08ca2f9443d215f Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 12 Feb 2018 16:02:06 +0100
Subject: [PATCH 1/2] added managevariantlist parser + updated
 makebedfordiagnostics

---
 makeBedForDiagnostics.sh | 21 ++++++++++++---------
 parseManVarList.sh       | 20 ++++++++++++++++++++
 2 files changed, 32 insertions(+), 9 deletions(-)
 create mode 100644 parseManVarList.sh

diff --git a/makeBedForDiagnostics.sh b/makeBedForDiagnostics.sh
index e10d293..ede4362 100644
--- a/makeBedForDiagnostics.sh
+++ b/makeBedForDiagnostics.sh
@@ -16,6 +16,7 @@ Options:
 	-h   Show this help.
 	-b   Name of the BED file
 	-n   Name of the new BED file
+	-w   Bedfile directory --> where to write to (default: this directory)
 	-e   Making BED file for exomekit true/false [default=false]
 ===============================================================================================================
 EOH
@@ -24,9 +25,9 @@ EOH
 }
 
 
-while getopts "b:d:e:h" opt;
+while getopts "b:n:e:w:h" opt;
 do
-	case $opt in h)showHelp;; b)bedfile="${OPTARG}";; n)name="${OPTARG}";; e)exome="${OPTARG}";;
+	case $opt in h)showHelp;; b)bedfile="${OPTARG}";; n)name="${OPTARG}";; w)workDir="${OPTARG}";; e)exome="${OPTARG}";;
 	esac
 done
 
@@ -51,6 +52,10 @@ if [[ -z "${exome:-}" ]]
 then
 	exome="false"
 fi
+if [[ -z "${workdir:-}" ]]
+then
+	workdir=$(pwd)
+fi
 
 
 if [ -d "/apps/data/Agilent/${name}" ]
@@ -63,22 +68,20 @@ then
 	exit 1
 fi
 
-thisDir=$(pwd)
 umcgDir=/apps/data/UMCG/Diagnostics/
 
-mkdir -p "${name}/human_g1k_v37/"
+mkdir -p "${workdir}/${name}/human_g1k_v37/"
 echo "created ${name}/human_g1k_v37/"
-cp "${bedfile}" "${name}"/
-echo "copied ${bedfile} ${name}/"
+cp "${bedfile}" "${workdir}/${name}"/
+echo "copied ${bedfile} ${workdir}/${name}/"
 ## navigate to folder
-cd "${name}"
+cd ${workdir}/"${name}"
 
 
 cp "${bedfile}" "human_g1k_v37/captured.bed"
 echo "copied ${bedfile} to human_g1k_v37/captured.bed"
 
 module load ngs-utils
-
 cd human_g1k_v37/
 
 ## Run the prepare step
@@ -97,7 +100,7 @@ else
 fi
 
 ##
-cd "${thisDir}"
+cd "${workdir}"
 echo "copied ${name} to ${umcgDir}"
 cp -r "${name}" ${umcgDir}
 
diff --git a/parseManVarList.sh b/parseManVarList.sh
new file mode 100644
index 0000000..f26965d
--- /dev/null
+++ b/parseManVarList.sh
@@ -0,0 +1,20 @@
+set -eu
+manList=$1
+
+ml ngs-utils
+EBROOTNGSMINUTILS=$HOME/github/ngs-utils
+if ls -d /apps/data/UMCG/ManVarList*  1> /dev/null 2>&1
+then
+	version=$(ls -d /apps/data/UMCG/ManVarList* | tail -1 | awk 'BEGIN {FS="_v"}{print $2+1}')
+else
+	version=1
+fi
+## UMCG-MVL_VKGLconsensusMVL-2017-11-27.txt
+awk '{print $1,$2}' "${manList}" \
+| awk -F ':' '{print $1"\t"$2"\t"$3"\t"$4}' | awk '{if ($2 ~ /-/){print $1"\t"$2"\t"$3}else {print $1"\t"$2"-"$2"\t"$3}}' | awk -F '-' '{print $1"\t"$2}' | awk '{print $1"\t"($2-1)"\t"$3"\t"$4}' |  sed '1d' > /apps/data/UMCG/ManVarList_v${version}_target.bed
+cd /apps/data/UMCG/
+
+sh ${EBROOTNGSMINUTILS}/makeBedForDiagnostics.sh -b ManVarList_v${version}_target.bed -n ManVarList_v${version} -w /apps/data/UMCG/
+
+cd -
+

From 1d623286163cc4d4c6a620471f61ae670c897f8c Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Tue, 13 Feb 2018 15:38:09 +0100
Subject: [PATCH 2/2] added printing rejected samples to file

---
 countCoverage.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/countCoverage.sh b/countCoverage.sh
index 95c8032..3f4fbbc 100644
--- a/countCoverage.sh
+++ b/countCoverage.sh
@@ -153,6 +153,7 @@ fi
 for i in "${REJECTEDSAMPLES[@]}"
 do
 	echo "removed ${WORKDIR}/coverage/${i}.coverage"
+	echo "removed ${WORKDIR}/coverage/${i}.coverage" > ${WORKDIR}/rejectedSamples.txt
 	rm ${WORKDIR}/coverage/${i}.coverage
 done