Merge pull request #282 from RoanKanninga/master

bugfix: coveragePerTarget other than capturingKit are not shown in th…

batchIDList_chr.csv

@@ -21,8 +21,7 @@ batchID
 20
 21
 22
-Xp
-Xnp
+X
 Y
 MT
 NC_001422.1

protocols/CoverageCalculations.sh

@@ -91,7 +91,7 @@ then
 		-T DepthOfCoverage \
 		-o "${sampleNameID}.${perTarget}.coveragePerTarget" \
 		-I "${dedupBam}" \
-                -mmq 20 \
+		-mmq 20 \
 		--omitDepthOutputAtEachBase \
 		-L "${perTargetDir}/${perTarget}.interval_list"
 
@@ -127,18 +127,16 @@ then
 			if [ $count == 0 ]
 			then
 				percentage=0
-
 			else
 				percentage=$(echo $((count*100/totalcount)))
 				if [ ${percentage%%.*} -gt 10 ]
 				then
-					echo "${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent, skipped"
-					echo "${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent, skipped" >> "${projectResultsDir}/coverage/${externalSampleID}.rejected"
-				else
-					rsync -a "${sampleNameID}.${perTarget}.coveragePerTarget.txt" "${projectResultsDir}/coverage/CoveragePerTarget/${Gender,,}/"
+					echo "WARNING: ${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent"
+					echo "WARNING: ${sampleNameID}: percentage $percentage ($count/$totalcount) is more than 10 procent" >> "${projectResultsDir}/coverage/${externalSampleID}.rejected"
 				fi
 			fi
 		fi
+		rsync -a "${sampleNameID}.${perTarget}.coveragePerTarget.txt" "${projectResultsDir}/coverage/CoveragePerTarget/${Gender,,}/"
 	done
 else
 	echo "There are no CoveragePerTarget calculations for this bedfile: ${bedfile}"

protocols/GenderCalculate.sh

@@ -18,7 +18,7 @@
 
 module load "${picardVersion}"
 
-if [[ "${capturedIntervals}" == *"ONCO_v"* || "${capturedIntervals}" == *"wgs"* || "${capturedIntervals}" == *"Targeted_v"*]]
+if [[ "${capturedIntervals}" == *"ONCO_v"* || "${capturedIntervals}" == *"wgs"* || "${capturedIntervals}" == *"Targeted_v"* ]]
 then
 	touch "${dedupBamMetrics}.noChrX"
 else

protocols/VariantCalling.sh

@@ -21,16 +21,16 @@
 
 #Function to check if array contains value
 array_contains () {
-    local array="$1[@]"
-    local seeking=$2
-    local in=1
-    for element in "${!array-}"; do
-        if [[ "${element}" == "${seeking}" ]]; then
-            in=0
-            break
-        fi
-    done
-    return "${in}"
+	local array="$1[@]"
+	local seeking="${2}"
+	local in=1
+	for element in "${!array-}"; do
+		if [[ "${element}" == "${seeking}" ]]; then
+			in=0
+			break
+		fi
+	done
+	return "${in}"
 }
 
 #Load GATK module
@@ -47,7 +47,7 @@ bams=()
 INPUTS=()
 for sampleID in "${externalSampleID[@]}"
 do
-        array_contains INPUTS "${sampleID}" || INPUTS+=("$sampleID")    # If bamFile does not exist in array add it
+	array_contains INPUTS "${sampleID}" || INPUTS+=("$sampleID")	# If bamFile does not exist in array add it
 done
 baitBatchLength=""
 sex=$(less "${projectResultsDir}/general/${externalSampleID}.chosenSex.txt" | awk 'NR==2')
@@ -68,33 +68,22 @@ else
 	genderCheck="Male"
 fi
 
-ploidy=""
+ploidy='2'
 myBed="${capturedBatchBed}"
 if [[ ! -f "${capturedBatchBed}" ||  ${baitBatchLength} -eq 0 ]]
 then
 	echo "skipped ${capturedBatchBed}, because the batch is empty or does not exist"
 else
-	if [ "${genderCheck}" == "Female" ]
+	if [[ "${capturedBatchBed}" == *batch-[0-9]*Y.bed || "${capturedBatchBed}" == *batch-Y.bed ]]
 	then
-		if [[ "${capturedBatchBed}" == *batch-[0-9]*Y.bed || "${capturedBatchBed}" == *batch-Y.bed ]]
+		if [ "${genderCheck}" == "Female" ]
 		then
-			echo -e "Female, chrY => ploidy=1\nbedfile=${femaleCapturedBatchBed}"
-			ploidy=1
+			echo "female, Y"
 			myBed="${femaleCapturedBatchBed}"
 		else
-			echo -e "Female, autosomal or chrX ==> ploidy=2"
-			ploidy=2
-		fi
-	elif [[ "${genderCheck}" == "Male" ]]
-	then
-		if [[ "${capturedBatchBed}" == *batch-[0-9]*Y.bed || "${capturedBatchBed}" == *batch-Y.bed || "${capturedBatchBed}" == *batch-Xnp.bed ]]
-		then
-			ploidy=1
-			echo -e "Male, chrY or chrXNonPar ==> ploidy=1"
-		else
-			ploidy=2
-			echo -e "Male, autosomal or chrXPar ==> ploidy=2"
+			echo "male, Y"
 		fi
+		ploidy=1	
 	fi
 
 	java -XX:ParallelGCThreads=1 -Djava.io.tmpdir="${tempDir}" -Xmx7g -jar \