Update tests

Makefile

@@ -12,7 +12,7 @@ STATIC=$(BIN2)/bamtocov $(BIN2)/bamtocounts $(BIN2)/covtotarget $(BIN2)/bamcount
 
 
 $(BIN)/%: $(SOURCE)/%.nim $(SOURCE)/covutils.nim bamtocov.nimble
-	nim c  $(NIM_PATHS) -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed  --out:$@ $<
+	nim c  $(NIM_PATHS) -d:NimblePkgVersion=$(VERSION) -d:danger --opt:speed  --out:$@ $<
 
 all: $(LIST)
 
@@ -27,8 +27,9 @@ $(BIN2)/%: $(SOURCE)/%.nim bamtocov.nimble ./hts_nim_static_builder
 	mkdir -p $(BIN2)
 	echo target: $@
 	echo base: $(shell basename $@)
-	./hts_nim_static_builder  -n bamtocov.nimble -s $< -- -d:NimblePkgVersion=2.7.0
+	./hts_nim_static_builder  -n bamtocov.nimble -s $< -- -d:NimblePkgVersion=$(VERSION)
 	mv ./$(shell basename $@) $(BIN2)
+
 test: testshpec
 
 testall: testbash testshpec testshunit2

Makefile.old

@@ -0,0 +1,41 @@
+# Create "make test"
+.PHONY: testshpec testshunit2 test clean build
+
+BIN=./bin
+SOURCE=./src
+NIM_PATHS= --colors:on --noNimblePath --path:/local/giovanni/bamtocov/nimbledeps/pkgs/hts-0.3.17 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/docopt-0.6.8 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/regex-0.19.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/unicodedb-0.9.0 --path:/local/giovanni/bamtocov/nimbledeps/pkgs/lapper-0.1.7 
+VERSION := $(shell grep version bamtocov.nimble  | grep  -o "[0-9]\\+\.[0-9]\.[0-9]\\+")
+LIST=$(BIN)/bamtocov $(BIN)/bamtoreads $(BIN)/bamtocounts $(BIN)/covtotarget $(BIN)/bamcountrefs $(BIN)/gff2bed $(BIN)/bamtocounts_legacy $(BIN)/bamtarget
+
+$(BIN)/%: $(SOURCE)/%.nim $(SOURCE)/covutils.nim bamtocov.nimble
+	nim c  $(NIM_PATHS) -d:NimblePkgVersion=$(VERSION) -d:release --opt:speed  --out:$@ $<
+
+all: $(LIST)
+
+
+test: testshpec 
+
+testall: testbash testshpec testshunit2
+testshpec:
+	@echo " --- Test shpec --- "
+	./tests/bin/shpec ./tests/shpec/bamtocov.sh
+
+testshunit2:
+	@echo " --- Test shunit2 --- "
+	./tests/unit/bamtocov-base.sh
+
+testbash:
+	@echo " --- Test (legacy) --- "
+	bash tests/all.sh
+
+
+build:
+	nimble build
+
+
+clean:
+	@echo "Cleaning..."
+	@for i in $(LIST); \
+	do \
+		if [ -e "$$i" ]; then rm -f $$i; echo "Removing $$i"; else echo "$$i Not found"; fi \
+	done

nim.cfg

@@ -2,7 +2,6 @@
 # nim c -a -d:static -d:release 
 
 -d:danger
--d:release
 --opt:speed
 @if static:
   passC:"-static"

tests/results/mini_wig250_max.wig

@@ -1,15 +1,15 @@
 fixedStep chrom=seq1 span=250
-0	5
-250	6
-500	1
-750	0
+5
+6
+1
+0
 fixedStep chrom=seq2 span=250
-0	0
-250	10
-500	10
-750	0
+0
+10
+10
+0
 fixedStep chrom=seq0 span=250
-0	0
-250	0
-500	0
-750	0
+0
+0
+0
+0

tests/shpec/bamtocov.sh

@@ -95,11 +95,11 @@ describe "Coverage tools tested by Shpec"
       LINES=$("$BINDIR"/bamtocov "$DATADIR"/mini.bam --wig 250 --op max | wc -l)
       assert equal $LINES 15
     end
-    it "Produces wig output (check lines at 750)"
-      LINES=$("$BINDIR"/bamtocov "$DATADIR"/mini.bam --wig 250 --op max | grep -w 750 | wc -l)
-      assert equal $LINES 3
+    it "Produces wig output (check coverage 10X)"
+      LINES=$("$BINDIR"/bamtocov "$DATADIR"/mini.bam --wig 250 --op max | grep -w 10 | wc -l)
+      assert equal $LINES 2
     end
-    it "Produces wig output (check lines at 1000 bases, unexpected)"
+    it "Produces wig output (check lines at 1000, unexpected)"
       LINES=$("$BINDIR"/bamtocov "$DATADIR"/mini.bam --wig 250 --op max |  grep -w 1000 |wc -l)
       assert equal $LINES 0
     end