c8174ac2c2237b3f8f24766ca50348487ba94fa7
galt
  Wed Aug 15 14:48:47 2012 -0700
bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size.  Matching is on chrom/start/end with name as an additional option for uniqueness.
diff --git src/utils/bedPileUps/makefile src/utils/bedPileUps/makefile
new file mode 100644
index 0000000..1fd85ac
--- /dev/null
+++ src/utils/bedPileUps/makefile
@@ -0,0 +1,33 @@
+include ../../inc/common.mk
+
+L += -lm -lz ${SOCKETLIB}
+MYLIBDIR = ../../lib/${MACHTYPE}
+MYLIBS = ${MYLIBDIR}/jkweb.a
+
+A = bedPileUps
+O = bedPileUps.o
+
+bedToBigBed: $O ${MYLIBS}
+	@${MKDIR} "${DESTDIR}${BINDIR}"
+	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
+	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+
+compile:: ${O} ${MYLIBS}
+	${CC} ${COPT} ${CFLAGS} -o ${A}${EXE} $O ${MYLIBS} ${L}
+
+clean::
+	rm -f ${O} ${A}
+	rm -fr tests/output
+
+test:
+	@rm -fr tests/output
+	@${MKDIR} tests/output
+	-${A} tests/input/foo.bed &> tests/output/foo.bed.txt
+	diff tests/expected/foo.bed.txt tests/output/foo.bed.txt
+	-${A} tests/input/foo2.bed &> tests/output/foo2.bed.txt
+	diff tests/expected/foo2.bed.txt tests/output/foo2.bed.txt
+	${A} tests/input/foo3.bed &> tests/output/foo3.bed.txt
+	diff tests/expected/foo3.bed.txt tests/output/foo3.bed.txt
+	${A} tests/input/foo4.bed &> tests/output/foo4.bed.txt
+	diff tests/expected/foo4.bed.txt tests/output/foo4.bed.txt
+	rm -fr tests/output