--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/htslib.mk	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,150 @@
+# Makefile rules useful for third-party code using htslib's public API.
+#
+#    Copyright (C) 2013-2015 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18@sanger.ac.uk>
+#
+# 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.
+
+# The makefile fragment included below provides variables that can be used
+# to express dependencies on headers supplied by an in-development htslib.
+# If your source file foo.c #includes <htslib/hts.h> and <htslib/kstring.h>,
+# you can write the correct prerequisites for foo.o as:
+#
+#	HTSDIR = <path to htslib top-level directory>
+#	include $(HTSDIR)/htslib.mk
+#
+#	foo.o: foo.c $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
+#
+# Variables are not provided for k*.h, as those never include other headers.
+
+HTSPREFIX = $(HTSDIR)/
+include $(HTSDIR)/htslib_vars.mk
+
+# Rules for rebuilding an in-development htslib's static and shared libraries.
+# If your program foo links with libhts, adding the appropriate prerequisite
+# will cause the library to be rebuilt as necessary:
+#
+#	foo: foo.o $(HTSDIR)/libhts.a
+#
+# or similarly if your target requires any of the tools supplied:
+#
+#	bar.bed.bgz.tbi: bar.bed.bgz $(HTSDIR)/tabix
+#		$(HTSDIR)/tabix -p bed bar.bed.bgz
+
+HTSLIB_PUBLIC_HEADERS = \
+	$(HTSDIR)/htslib/bgzf.h \
+	$(HTSDIR)/htslib/faidx.h \
+	$(HTSDIR)/htslib/hfile.h \
+	$(HTSDIR)/htslib/hts.h \
+	$(HTSDIR)/htslib/hts_defs.h \
+	$(HTSDIR)/htslib/khash.h \
+	$(HTSDIR)/htslib/klist.h \
+	$(HTSDIR)/htslib/knetfile.h \
+	$(HTSDIR)/htslib/kseq.h \
+	$(HTSDIR)/htslib/ksort.h \
+	$(HTSDIR)/htslib/kstring.h \
+	$(HTSDIR)/htslib/regidx.h \
+	$(HTSDIR)/htslib/sam.h \
+	$(HTSDIR)/htslib/synced_bcf_reader.h \
+	$(HTSDIR)/htslib/tbx.h \
+	$(HTSDIR)/htslib/vcf.h \
+	$(HTSDIR)/htslib/vcf_sweep.h \
+	$(HTSDIR)/htslib/vcfutils.h
+
+HTSLIB_ALL = \
+	$(HTSLIB_PUBLIC_HEADERS) \
+	$(HTSDIR)/bgzf.c \
+	$(HTSDIR)/faidx.c \
+	$(HTSDIR)/hfile_internal.h \
+	$(HTSDIR)/hfile.c \
+	$(HTSDIR)/hfile_irods.c \
+	$(HTSDIR)/hfile_net.c \
+	$(HTSDIR)/hts.c \
+	$(HTSDIR)/knetfile.c \
+	$(HTSDIR)/kstring.c \
+	$(HTSDIR)/regidx.c \
+	$(HTSDIR)/sam.c \
+	$(HTSDIR)/synced_bcf_reader.c \
+	$(HTSDIR)/tbx.c \
+	$(HTSDIR)/vcf.c \
+	$(HTSDIR)/vcf_sweep.c \
+	$(HTSDIR)/vcfutils.c \
+	$(HTSDIR)/cram/cram.h \
+	$(HTSDIR)/cram/cram_codecs.c \
+	$(HTSDIR)/cram/cram_codecs.h \
+	$(HTSDIR)/cram/cram_decode.c \
+	$(HTSDIR)/cram/cram_decode.h \
+	$(HTSDIR)/cram/cram_encode.c \
+	$(HTSDIR)/cram/cram_encode.h \
+	$(HTSDIR)/cram/cram_index.c \
+	$(HTSDIR)/cram/cram_index.h \
+	$(HTSDIR)/cram/cram_io.c \
+	$(HTSDIR)/cram/cram_io.h \
+	$(HTSDIR)/cram/cram_samtools.c \
+	$(HTSDIR)/cram/cram_samtools.h \
+	$(HTSDIR)/cram/cram_stats.c \
+	$(HTSDIR)/cram/cram_stats.h \
+	$(HTSDIR)/cram/cram_structs.h \
+	$(HTSDIR)/cram/files.c \
+	$(HTSDIR)/cram/mFILE.c \
+	$(HTSDIR)/cram/mFILE.h \
+	$(HTSDIR)/cram/md5.c \
+	$(HTSDIR)/cram/md5.h \
+	$(HTSDIR)/cram/misc.h \
+	$(HTSDIR)/cram/open_trace_file.c \
+	$(HTSDIR)/cram/open_trace_file.h \
+	$(HTSDIR)/cram/os.h \
+	$(HTSDIR)/cram/pooled_alloc.c \
+	$(HTSDIR)/cram/pooled_alloc.h \
+	$(HTSDIR)/cram/sam_header.c \
+	$(HTSDIR)/cram/sam_header.h \
+	$(HTSDIR)/cram/string_alloc.c \
+	$(HTSDIR)/cram/string_alloc.h \
+	$(HTSDIR)/cram/thread_pool.c \
+	$(HTSDIR)/cram/thread_pool.h \
+	$(HTSDIR)/cram/vlen.c \
+	$(HTSDIR)/cram/vlen.h \
+	$(HTSDIR)/cram/zfio.c \
+	$(HTSDIR)/cram/zfio.h
+
+$(HTSDIR)/libhts.a: $(HTSLIB_ALL)
+	+cd $(HTSDIR) && $(MAKE) lib-static
+
+$(HTSDIR)/libhts.so $(HTSDIR)/libhts.dylib: $(HTSLIB_ALL)
+	+cd $(HTSDIR) && $(MAKE) lib-shared
+
+$(HTSDIR)/bgzip: $(HTSDIR)/bgzip.c $(HTSLIB_PUBLIC_HEADERS)
+	+cd $(HTSDIR) && $(MAKE) bgzip
+
+$(HTSDIR)/htsfile: $(HTSDIR)/htsfile.c $(HTSLIB_PUBLIC_HEADERS)
+	+cd $(HTSDIR) && $(MAKE) htsfile
+
+$(HTSDIR)/tabix: $(HTSDIR)/tabix.c $(HTSLIB_PUBLIC_HEADERS)
+	+cd $(HTSDIR) && $(MAKE) tabix
+
+# Rules for phony targets.  You may wish to have your corresponding phony
+# targets invoke these in addition to their own recipes:
+#
+#	clean: clean-htslib
+
+clean-htslib install-htslib:
+	+cd $(HTSDIR) && $(MAKE) $(@:-htslib=)
+
+.PHONY: clean-htslib install-htslib