--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/Makefile	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,133 @@
+# Makefile for ezBAMQC, utilities for the Sequence Alignment/Map format.
+#
+#    Version 0.6.5
+#
+#    Copyright (C) 2015 Bioinformatics Shared Resource, CSHL.
+#    Portions copyright (C) 2015 Cold Spring Harbor Laboratory.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+CC       = g++
+CPPFLAGS = $(DFLAGS) $(INCLUDES)
+CFLAGS   = -g -fpermissive -Wall -O9 -O3 -std=c++11 -fPIC 
+LDFLAGS  = -O9 -fpermissive
+LDLIBS   =
+DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+LOBJS=      src/ezBAMQC/GeneFeatures.o src/ezBAMQC/rRNA.o src/ezBAMQC/IntervalTree.o src/ezBAMQC/InnerDist_prof.o \
+            src/ezBAMQC/Results.o src/ezBAMQC/Mappability.o src/ezBAMQC/Coverage_prof.o src/ezBAMQC/parseBAM.o
+
+INCLUDES=   -I$(HTSDIR)
+LIBCURSES=  -lcurses # -lXCurses
+
+prefix      = /usr/local
+exec_prefix = $(prefix)
+bindir      = $(exec_prefix)/bin
+mandir      = $(prefix)/share/man
+man1dir     = $(mandir)/man1
+
+MKDIR_P = mkdir -p
+#INSTALL = install -p
+#INSTALL_PROGRAM = $(INSTALL)
+#INSTALL_DATA    = $(INSTALL) -m 644
+#INSTALL_DIR     = $(MKDIR_P) -m 755
+
+
+PROGRAMS = libBAMqc.so
+
+
+all: $(PROGRAMS)
+
+
+# Adjust $(HTSDIR) to point to your top-level htslib directory
+HTSDIR = ./src/htslib
+include $(HTSDIR)/htslib.mk
+HTSLIB = $(HTSDIR)/libhts.a
+BGZIP  = $(HTSDIR)/bgzip
+
+
+PACKAGE_VERSION = 0.5
+
+
+.SUFFIXES: .cpp .o
+
+.cpp.o:
+	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+
+
+#lib:libbam.a
+
+#libbam.a:$(LOBJS)
+#	$(AR) -csru $@ $(LOBJS)
+
+#libBAMqc.so: $(LOBJS) $(HTSLIB)
+#	$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
+
+libBAMqc.so: $(LOBJS) $(HTSLIB)
+#	$(CC) -shared -Wl,-soname, libBAMqc.so.$(PACKAGE_VERSION) -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
+	$(CC) -shared  -lpthread $(LDFLAGS) -o $@ $(LOBJS) $(HTSLIB) $(LDLIBS) -lz -lm
+#	ln -sf $@ libBAMqc.so.$(PACKAGE_VERSION)
+
+Constants_h = src/ezBAMQC/Constants.h
+IntervalTree_h = src/ezBAMQC/IntervalTree.h $(Constants_h)
+GeneFeatures_h = src/ezBAMQC/GeneFeatures.h $(Constants_h)
+rRNA_h = src/ezBAMQC/rRNA.h $(IntervalTree_h) $(GeneFeatures_h)
+Results_h = src/ezBAMQC/Resualts.h
+Mappability_h = src/ezBAMQC/Mappability.h $(Constants_h)
+InnerDist_prof_h = src/ezBAMQC/InnerDist_prof.h $(GeneFeatures_h)
+Coverage_prof_h = src/ezBAMQC/Coverage_prof.h $(GeneFeatures_h)
+parseBAM_h = src/ezBAMQC/parseBAM.h
+
+
+IntervalTree.o: src/ezBAMQC/IntervalTree.cpp $(IntervalTree_h)
+GeneFeatures.o: src/ezBAMQC/GeneFeatures.cpp $(GeneFeatures_h)
+rRNA.o: src/ezBAMQC/rRNA.cpp $(rRNA_h)
+Results.o: src/ezBAMQC/Results.cpp $(Results_h)
+Mappability.o: src/ezBAMQC/Mappability.cpp $(Mappability_h) $(htslib_sam_h)
+InnerDist_prof.o: src/ezBAMQC/InnerDist_prof.cpp $(InnerDist_prof_h) $(htslib_sam_h)
+Coverage_prof.o: src/ezBAMQC/Coverage_prof.cpp $(Coverage_prof_h)
+parseBAM.o: src/ezBAMQC/parseBAM.cpp $(parseBAM_h) $(htslib_sam_h) $(GeneFeatures_h) $(rRNA_h) $(Mappability_h) $(Coverage_prof_h) $(InnerDist_prof_h)
+
+
+#install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
+#	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
+#	$(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
+#	$(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)
+
+
+mostlyclean:
+	-rm -f src/*.o
+
+clean: mostlyclean
+	-rm -f $(PROGRAMS)
+
+distclean: clean
+	-rm -f TAGS
+
+clean-all: clean
+
+
+tags:
+	ctags -f TAGS *.[ch] misc/*.[ch]
+
+
+force:
+
+
+.PHONY: all clean clean-all distclean force 
+.PHONY: mostlyclean tags