Merge pull request #179 from RoanKanninga/master

small fixes to make bed file script

makeBedForDiagnostics.sh

@@ -16,7 +16,7 @@ Options:
 	-h   Show this help.
 	-b   Name of the BED file
 	-n   Name of the new BED file
-	-e   Making BED file for exomekit [default=false]
+	-e   Making BED file for exomekit true/false [default=false]
 ===============================================================================================================
 EOH
 	trap - EXIT
@@ -26,7 +26,7 @@ EOH
 
 while getopts "b:d:e:h" opt;
 do
-	case $opt in h)showHelp;; b)bedfile="${OPTARG}";; d)name="${OPTARG}";; e)exome="${OPTARG}";;
+	case $opt in h)showHelp;; b)bedfile="${OPTARG}";; n)name="${OPTARG}";; e)exome="${OPTARG}";;
 	esac
 done
 
@@ -50,8 +50,6 @@ fi
 if [[ -z "${exome:-}" ]]
 then
 	exome="false"
-else
-	exome="true"
 fi
 
 
@@ -87,11 +85,15 @@ cd human_g1k_v37/
 
 if [[ "${exome}" == 'true' ]]
 then
-	echo 'Creating bedfiles for a new exomekit ${name}'
+	echo "Creating bedfiles for a new exomekit ${name}"
 	sh ${EBROOTNGSMINUTILS}/prepare_NGS_Bedfiles.sh -n captured
-else
+elif [[ "${exome}" == 'false' ]]
+then
 	echo "Creating bedfiles for a new kit ${name}"
 	sh ${EBROOTNGSMINUTILS}/prepare_NGS_Bedfiles.sh -n captured -c true -d targeted
+else
+	echo "please fill in true or false"
+	exit 1
 fi
 
 ##
@@ -105,13 +107,13 @@ rename "captured" "${name}" "captured."*
 
 #perbase
 cd "${umcgDir}/CoveragePerBase/"
-mkdir "${name}"
+mkdir -p "${name}"
 cd "${name}"
 ln -sf "../../${name}"/
 
 #pertarget
 cd "${umcgDir}/CoveragePerTarget/"
-mkdir "${name}"
+mkdir -p "${name}"
 cd "${name}"
 ln -sf "../../${name}"/
 

prepare_NGS_Bedfiles.sh

@@ -220,8 +220,6 @@ then
 
 		sort -V -k1 -k2 -k3 ${TMP}/${NAME}.per_base.bed | uniq > ${baits}.uniq.per_base.bed.tmp
 		sort -V ${baits}.uniq.per_base.bed.tmp > ${baits}.uniq.per_base.bed
-		#rm ${baits}.uniq.per_base.bed.tmp
-		#rm ${TMP}/${NAME}.per_base.bed
 
 		echo "per base done: ${baits}.uniq.per_base.bed"
 	else
@@ -276,18 +274,18 @@ then
 		batchIntervallistDir=${MAP}
 		chrXNONPARBed=${baits}.batch-Xnp.bed
 		chrXPARBed=${baits}.batch-Xp.bed
-		
+
 		##Lastline is always phiX, we want to know whi
-		LASTLINE=$(tail -n1 ${baits}.bed)
-		if [[ $LASTLINE == *"NC_"* ]]
+		FIRSTLINE=$(head -1 ${baits}.merged.bed)
+		if [[ "${FIRSTLINE}" == *"NC_"* ]]
 		then
-			chromo=$(echo "${LASTLINE}" | awk '{FS=" "}{print $1}')
-			position=$(echo "${LASTLINE}" | awk '{FS=" "}{print $2}')
+			chromo=$(echo "${FIRSTLINE}" | awk '{FS=" "}{print $1}')
+			position=$(echo "${FIRSTLINE}" | awk '{FS=" "}{print $2}')
 		else
-			chromo=$(tail -n2 ${baits}.bed | head -1 | awk '{FS=" "}{print $1}')
-                        position=$(tail -n2 ${baits}.bed | head -1 | awk '{FS=" "}{print $2}')
-
+			chromo=$(head -2 ${baits}.merged.bed | tail -1 | awk '{FS=" "}{print $1}')
+                        position=$(head -2 ${baits}.merged.bed | tail -1 | awk '{FS=" "}{print $2}')
 		fi
+
 		awk '{
 			if ($1 == "X"){
 				if (($2 == 1) && ($3 == 155270560)){
@@ -308,18 +306,8 @@ then
 				print $0 >> "captured.batch-"$1".bed"
 			}
 		}' ${baits}.merged.bed
-		### Check where to put the phiXref
-		if [ "${chromo}" == "X" ]
-		then
-			if [[ ${position} -gt 60001 && ${position} -lt 2699520 ]] || [[ $position -gt 154931044 && $position -lt 155260560 ]]
-			then
-				echo -e "NC_001422.1\t1\t5386\tphiX174" >> captured.batch-Xp.bed
-			else
-				echo -e "NC_001422.1\t1\t5386\tphiX174" >> captured.batch-Xnp.bed
-			fi 
-		else
-			echo -e "NC_001422.1\t1\t5386\tphiX174" >> captured.batch-${chromo}.bed
-		fi
+
+		echo -e "NC_001422.1\t1\t5386\tphiX174" >> captured.batch-${chromo}.bed
 	fi
 else
 	if [ -f ${baits}.batch-1.bed ]
@@ -383,8 +371,7 @@ else
 		echo "PAR DONE"
 		BATCH_ALL=$((BATCHCOUNT + batchCount_X))
 		#move the X chromosome folders
-		lengthR=`less ${phiXRef} | wc -l`
-		echo "lengthR: $lengthR"
+		lengthR=$(less ${phiXRef} | wc -l)
 		lengthRef=$(( ${lengthR} + 2 ))
 		if [ ${lengthOFChrXNP1} -ne ${lengthOFChrXNP2} ]
 		then
@@ -395,11 +382,9 @@ else
 				echo "ba=$ba bi=$bi"
 				if [[ ${i} -lt 10 ]]
 				then
-					echo "$i is minder dan 10"
 					mv  ${batchIntervallistDir}/temp_000${i}_of_${batchCount_X}/scattered.intervals  ${ba}.interval_list 
 					tail -n+${lengthRef} ${ba}.interval_list > ${ba}.bed
 				else
-					echo "$i is meer dan 10"
 					mv  ${batchIntervallistDir}/temp_00${i}_of_${batchCount_X}/scattered.intervals  ${ba}.interval_list
 					tail -n+${lengthRef} ${ba}.interval_list > ${ba}.bed
 				fi
@@ -493,5 +478,3 @@ then
 		echo -e 'Y\t1\t2\t+\tFake' > ${MAP}/captured.femaleY.bed
 	fi
 fi
-
-#for f in ${MAP}/*_baits_*; do cp $f ${f/_baits_/_exons_}; done