From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: allow for using packaged htscodecs
--- staden-io-lib.orig/Makefile.am
+++ staden-io-lib/Makefile.am
@@ -32,7 +32,7 @@
 AUTOMAKE_OPTIONS = foreign no-dependencies
 ACLOCAL_AMFLAGS = -I m4
 
-SUBDIRS = htscodecs io_lib progs tests
+SUBDIRS = io_lib progs tests
 
 man_MANS = \
 	man/man1/srf_index_hash.1 \
--- staden-io-lib.orig/io_lib/Makefile.am
+++ staden-io-lib/io_lib/Makefile.am
@@ -134,6 +134,6 @@
 	bgzip.h \
 	cram_block_compression.h
 
-libstaden_read_la_CPPFLAGS = -I${top_srcdir} -I${top_srcdir}/htscodecs @LIBCURL_CPPFLAGS@
+libstaden_read_la_CPPFLAGS = -I${top_srcdir} @LIBCURL_CPPFLAGS@
 libstaden_read_la_LDFLAGS = -version-info @VERS_CURRENT@:@VERS_REVISION@:@VERS_AGE@ 
-libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@ ${top_builddir}/htscodecs/htscodecs/libhtscodecs.la
+libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@ -lhtscodecs
--- staden-io-lib.orig/progs/Makefile.am
+++ staden-io-lib/progs/Makefile.am
@@ -147,4 +147,4 @@
 cram_filter_SOURCES = cram_filter.c
 cram_filter_LDADD = $(top_builddir)/io_lib/libstaden-read.la
 
-AM_CPPFLAGS= -I${top_srcdir} -I${top_srcdir}/htscodecs 
+AM_CPPFLAGS= -I${top_srcdir}
--- staden-io-lib.orig/tests/Makefile.am
+++ staden-io-lib/tests/Makefile.am
@@ -58,7 +58,7 @@
 cram_io_test_SOURCES = cram_io_test.c
 cram_io_test_LDADD = $(top_builddir)/io_lib/libstaden-read.la
 
-AM_CPPFLAGS= -I${top_srcdir} -I${top_srcdir}/htscodecs
+AM_CPPFLAGS= -I${top_srcdir}
 
 # Scram and scram_mt are the same input and output,
 # but with different options.  Hence they clash and cannot run
