added --typical/--megarow/--float128 test loop

Makefile

@@ -20,9 +20,9 @@ export BINARY_TYPE     = ${DEFAULT_BINARY_TYPE}
 DEBUG_TYPE             = ${TYPICAL}
 WRAPPERS               = $(wildcard ${APPDIR}/conversion/src/wrappers/*)
 CWD                   := $(shell pwd)
-BINDIR                 = bin
+export BINDIR          = $(CWD)/bin
 BINDIR_MODULE          = modules
-
+export DESTBINDIR      = .
 
 default:
 ifeq ($(KERNEL), Darwin)
@@ -45,7 +45,7 @@ all:
 	$(MAKE) megarow -f ${SELF}
 	$(MAKE) float128 -f ${SELF}
 	$(MAKE) install_all -f ${SELF}
-	$(MAKE) symlink_typical -f ${SELF}
+	$(MAKE) symlink_post_install_all -f ${SELF}
 
 module_all:
 	$(MAKE) support -f ${SELF}
@@ -64,6 +64,10 @@ megarow:
 typical:
 	$(MAKE) BINARY_TYPE=$(TYPICAL) -f ${SELF}
 
+symlink_post_install_all:
+	cd ${BINDIR} && ./switch-BEDOPS-binary-type --typical .
+	cd ${CWD}
+
 symlink_typical:
 	$(eval SRCNAMES=`find $(BINDIR)/ -maxdepth 1 -mindepth 1 -type f -name '*$(TYPICAL)' -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`)
 	for SRCNAME in ${SRCNAMES}; do \

applications/other/switch-BEDOPS-binary-type

@@ -83,6 +83,7 @@ then
     TYPE=float128
 fi
 
+echo $BINDIR
 for SRCNAME in `find ${BINDIR} -maxdepth 1 -mindepth 1 -type f -name "*${TYPE}" -print0 | xargs -L1 -0 -I{} sh -c 'basename {}'`
 do
     DESTNAME=`echo ${SRCNAME} | perl -Tpe 's/-'${TYPE}'//'`

tests/Makefile

@@ -1,6 +1,21 @@
 CWD := $(shell pwd)
+SWITCH = $(CWD)/../bin/switch-BEDOPS-binary-type
+ALL_BINARY_TYPES = typical megarow float128
 
-all: bedops
+all: tests
 
-bedops:
-	$(MAKE) all -C $(CWD)/tests/bedops
+.PHONY: tests bedops
+
+tests:
+	$(MAKE) bedops -C $(CWD)/tests
+	$(MAKE) clean -C $(CWD)/tests
+
+bedops: 
+	for btype in ${ALL_BINARY_TYPES}; do \
+		$(SWITCH) --$$btype $(BINDIR) || exit $$?; \
+		$(MAKE) all -C $(CWD)/bedops BUILDTYPE=$$btype; \
+	done
+
+clean:
+	$(SWITCH) --typical $(BINDIR)
+	@rm -rf /tmp/tmp.*

tests/bedops/Makefile

@@ -1,25 +1,25 @@
 APP = bedops
 CWD := $(abspath $(patsubst %/,%,$(dir $(abspath $(lastword $(MAKEFILE_LIST))))))
 BIN = $(CWD)/../../bin/bedops
-TMPDIR := $(shell mktemp -d)
+TMP := $(shell mktemp -d)
 
 all: 
-	@echo "Testing [$(APP)]"
+	@echo "Testing binary [$(APP)] and build type [$(BUILDTYPE)]"
 	@$(MAKE) operations
-	@$(MAKE) clean
 
 operations: prep merge
 
 prep:
-	@[ -f $(BIN) ] || echo "Missing [$(APP)]"
+	@[ -f $(BIN) ] || echo "Missing binary [$(APP)] for build type [$(BUILDTYPE)]"
+	@echo "Writing to [$(TMP)]"
 	$(BIN) --version
 
 merge:
-	@echo "[$(APP) --$@]"
-	@echo "[$(APP) --$@] - [001]"
-	@$(BIN) -m $(CWD)/data/001.merge.001.test > $(TMPDIR)/001.merge.001.observed
-	@diff -s $(TMPDIR)/001.merge.001.observed $(CWD)/data/001.merge.001.expected
-
-clean:
-	@echo "Cleaning [$(APP)] test results..."
-	@rm -rf $(TMPDIR)
+#	Test 001
+	@echo "[$(APP)-$(BUILDTYPE) --$@] - [Test 001]"
+	@$(BIN) -m $(CWD)/data/001.merge.001.test > $(TMP)/001.merge.001.observed
+	@diff -s $(TMP)/001.merge.001.observed $(CWD)/data/001.merge.001.expected
+#	Test 002
+	@echo "[$(APP)-$(BUILDTYPE) --$@] - [Test 002]"
+	@$(BIN) -m $(CWD)/data/001.merge.001.test $(CWD)/data/002.complement.001.expected > $(TMP)/006.merge.002.observed
+	@diff -s $(TMP)/006.merge.002.observed $(CWD)/data/006.merge.002.expected

tests/bedops/data/002.complement.001.expected

@@ -0,0 +1,2 @@
+chr7	102	105
+chr7	116	117

tests/bedops/data/006.merge.002.expected

@@ -0,0 +1 @@
+chr7	2	151