use samtools in config and for cnvnator_wrapper

Makefile

@@ -54,6 +54,7 @@ config:
 	@echo "SPEEDSEQ_HOME=$(MKFILE_DIR)" >> $(TARGET_BIN)/speedseq.config
 	@echo "" >> $(TARGET_BIN)/speedseq.config
 	@echo "# general" >> $(TARGET_BIN)/speedseq.config
+	@echo "SAMTOOLS=`which samtools`" >> $(TARGET_BIN)/speedseq.config
 	@echo "SAMBAMBA=$(MKFILE_DIR)/$(TARGET_BIN)/sambamba" >> $(TARGET_BIN)/speedseq.config
 	@echo "BGZIP=$(MKFILE_DIR)/$(TARGET_BIN)/bgzip" >> $(TARGET_BIN)/speedseq.config
 	@echo "TABIX=$(MKFILE_DIR)/$(TARGET_BIN)/tabix" >> $(TARGET_BIN)/speedseq.config

bin/speedseq

@@ -27,6 +27,7 @@ function source_binaries() {
 	# general
 	SPEEDSEQ_HOME=$( dirname `which speedseq` )
 	SAMBAMBA=`which sambamba || true`
+	SAMTOOLS=`which samtools || true`
 	BGZIP=`which bgzip || true`
 	TABIX=`which tabix || true`
 	VAWK=`which vawk || true`
@@ -1524,10 +1525,10 @@ global options:
 	    then
 		echo "
     # run cnvnator-multi
-    $PYTHON $CNVNATOR_WRAPPER --cnvnator $CNVNATOR_MULTI -T $TEMP_DIR/cnvnator-temp -t $THREADS -w $WINDOW_SIZE -b ${FULL_BAM} -o $TEMP_DIR/$FULL_BASE.readdepth -c $CNVNATOR_CHROMS_DIR -g GRCh37
+    $PYTHON $CNVNATOR_WRAPPER --samtools $SAMTOOLS --cnvnator $CNVNATOR_MULTI -T $TEMP_DIR/cnvnator-temp -t $THREADS -w $WINDOW_SIZE -b ${FULL_BAM} -o $TEMP_DIR/$FULL_BASE.readdepth -c $CNVNATOR_CHROMS_DIR
 		"
 	    fi
-	    $PYTHON $CNVNATOR_WRAPPER --cnvnator $CNVNATOR_MULTI -T $TEMP_DIR/cnvnator-temp -t $THREADS -w $WINDOW_SIZE -b ${FULL_BAM} -o $TEMP_DIR/$FULL_BASE.readdepth -c $CNVNATOR_CHROMS_DIR -g GRCh37
+	    $PYTHON $CNVNATOR_WRAPPER --samtools $SAMTOOLS --cnvnator $CNVNATOR_MULTI -T $TEMP_DIR/cnvnator-temp -t $THREADS -w $WINDOW_SIZE -b ${FULL_BAM} -o $TEMP_DIR/$FULL_BASE.readdepth -c $CNVNATOR_CHROMS_DIR
 
 	    # Calculate read-depth of LUMPY calls
 	    if [[ "$VERBOSE" -eq 1 ]]