Remove internal dependency on htslib

Author: julianhess

Makefile.am

@@ -1,5 +1,5 @@
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = bwa htslib fermi-lite src
+SUBDIRS = bwa fermi-lite src
 
 install:  
 	mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib

Makefile.in

@@ -1,7 +1,7 @@
-# Makefile.in generated by automake 1.16.1 from Makefile.am.
+# Makefile.in generated by automake 1.15 from Makefile.am.
 # @configure_input@
 
-# Copyright (C) 1994-2018 Free Software Foundation, Inc.
+# Copyright (C) 1994-2014 Free Software Foundation, Inc.
 
 # This Makefile.in is free software; the Free Software Foundation
 # gives unlimited permission to copy and/or distribute it,
@@ -132,7 +132,7 @@ am__recursive_targets = \
   $(RECURSIVE_CLEAN_TARGETS) \
   $(am__extra_recursive_targets)
 AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
-	cscope distdir distdir-am dist dist-all distcheck
+	cscope distdir dist dist-all distcheck
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
 	$(LISP)config.h.in
 # Read a list of newline-separated strings from the standard input,
@@ -285,6 +285,7 @@ pdfdir = @pdfdir@
 prefix = @prefix@
 program_transform_name = @program_transform_name@
 psdir = @psdir@
+runstatedir = @runstatedir@
 sbindir = @sbindir@
 sharedstatedir = @sharedstatedir@
 srcdir = @srcdir@
@@ -294,7 +295,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = bwa htslib fermi-lite src
+SUBDIRS = bwa fermi-lite src
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 
@@ -320,8 +321,8 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	    echo ' $(SHELL) ./config.status'; \
 	    $(SHELL) ./config.status;; \
 	  *) \
-	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles)'; \
-	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__maybe_remake_depfiles);; \
+	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe)'; \
+	    cd $(top_builddir) && $(SHELL) ./config.status $@ $(am__depfiles_maybe);; \
 	esac;
 
 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
@@ -454,10 +455,7 @@ distclean-tags:
 	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
 	-rm -f cscope.out cscope.in.out cscope.po.out cscope.files
 
-distdir: $(BUILT_SOURCES)
-	$(MAKE) $(AM_MAKEFLAGS) distdir-am
-
-distdir-am: $(DISTFILES)
+distdir: $(DISTFILES)
 	$(am__remove_distdir)
 	test -d "$(distdir)" || mkdir "$(distdir)"
 	@srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
@@ -522,7 +520,7 @@ distdir-am: $(DISTFILES)
 	  ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \
 	|| chmod -R a+r "$(distdir)"
 dist-gzip: distdir
-	tardir=$(distdir) && $(am__tar) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).tar.gz
+	tardir=$(distdir) && $(am__tar) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).tar.gz
 	$(am__post_remove_distdir)
 
 dist-bzip2: distdir
@@ -548,7 +546,7 @@ dist-shar: distdir
 	@echo WARNING: "Support for shar distribution archives is" \
 	               "deprecated." >&2
 	@echo WARNING: "It will be removed altogether in Automake 2.0" >&2
-	shar $(distdir) | eval GZIP= gzip $(GZIP_ENV) -c >$(distdir).shar.gz
+	shar $(distdir) | GZIP=$(GZIP_ENV) gzip -c >$(distdir).shar.gz
 	$(am__post_remove_distdir)
 
 dist-zip: distdir
@@ -566,7 +564,7 @@ dist dist-all:
 distcheck: dist
 	case '$(DIST_ARCHIVES)' in \
 	*.tar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).tar.gz | $(am__untar) ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\
 	*.tar.bz2*) \
 	  bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\
 	*.tar.lz*) \
@@ -576,7 +574,7 @@ distcheck: dist
 	*.tar.Z*) \
 	  uncompress -c $(distdir).tar.Z | $(am__untar) ;;\
 	*.shar.gz*) \
-	  eval GZIP= gzip $(GZIP_ENV) -dc $(distdir).shar.gz | unshar ;;\
+	  GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\
 	*.zip*) \
 	  unzip $(distdir).zip ;;\
 	esac

SeqLib/BamHeader.h

@@ -1,10 +1,10 @@
 #ifndef SEQLIB_BAM_HEADER_H__
 #define SEQLIB_BAM_HEADER_H__
 
-#include "htslib/htslib/hts.h"
-#include "htslib/htslib/sam.h"
-#include "htslib/htslib/bgzf.h"
-#include "htslib/htslib/kstring.h"
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/bgzf.h>
+#include <htslib/kstring.h>
 
 #include "SeqLib/SeqLibUtils.h"
 #include <string>

SeqLib/BamRecord.h

@@ -10,11 +10,11 @@
 #include <algorithm>
 
 extern "C" {
-#include "htslib/htslib/hts.h"
-#include "htslib/htslib/sam.h"
-#include "htslib/htslib/bgzf.h"
-#include "htslib/htslib/kstring.h"
-#include "htslib/htslib/faidx.h"
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/bgzf.h>
+#include <htslib/kstring.h>
+#include <htslib/faidx.h>
 
 }
 

SeqLib/BamWalker.h

@@ -12,8 +12,7 @@
 #endif
 
 extern "C" {
-#include "htslib/cram/cram.h"
-#include "htslib/cram/cram_io.h"
+#include <htslib/cram.h>
 }
 
 struct idx_delete {

SeqLib/RefGenome.h

@@ -5,7 +5,7 @@
 #include <cstdlib>
 #include <iostream>
 
-#include "htslib/htslib/faidx.h"
+#include <htslib/faidx.h>
 
 namespace SeqLib {