Author: Andreas Tille <tille@debian.org>
Last-Update: 2021-01-28
Description: Use Debian packaged libfastahack (and libdisorder)
Forwarded: not-needed
--- libvcflib.orig/CMakeLists.txt
+++ libvcflib/CMakeLists.txt
@@ -33,6 +33,7 @@
 pkg_check_modules(HTSLIB htslib)
 pkg_check_modules(TABIXPP tabixpp) # Optional
 pkg_check_modules(SMITHWATERMAN REQUIRED IMPORTED_TARGET libsmithwaterman)
+pkg_check_modules(FASTAHACK REQUIRED IMPORTED_TARGET libfastahack)
 
 # ---- Build switches
 
@@ -54,7 +55,6 @@
 # ---- Include files
 
 include_directories(include)
-include_directories(fastahack)
 include_directories(intervaltree)
 include_directories(multichoose)
 include_directories(filevercmp)
@@ -70,7 +70,6 @@
   src/*.h*
   multichoose/*.h*
   intervaltree/*.h*
-  fastahack/*.h*
   filevercmp/*.h*)
 
 add_library(vcflib STATIC
@@ -89,12 +88,12 @@
     src/split.cpp
     src/ssw.hpp
     src/ssw_cpp.hpp
-    fastahack/Fasta.cpp
     filevercmp/filevercmp.c
     )
 
 target_link_libraries(vcflib
     PkgConfig::SMITHWATERMAN
+    PkgConfig::FASTAHACK
     )
 
 set(BINS
--- libvcflib.orig/src/Variant.h
+++ libvcflib/src/Variant.h
@@ -31,7 +31,7 @@
 #include "ssw_cpp.hpp"
 #include "convert.h"
 #include "multichoose.h"
-#include <Fasta.h>
+#include <fastahack/Fasta.h>
 extern "C" {
     #include "filevercmp.h"
 }
--- libvcflib.orig/src/vcf2dag.cpp
+++ libvcflib/src/vcf2dag.cpp
@@ -11,7 +11,7 @@
 #include "BedReader.h"
 #include "IntervalTree.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <algorithm>
 #include <list>
 #include <set>
--- libvcflib.orig/src/vcf2fasta.cpp
+++ libvcflib/src/vcf2fasta.cpp
@@ -13,7 +13,7 @@
 #include "split.h"
 #include <set>
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <iostream>
 #include <fstream>
 
--- libvcflib.orig/src/vcfcheck.cpp
+++ libvcflib/src/vcfcheck.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include "gpatInfo.hpp"
 #include <getopt.h>
 
--- libvcflib.orig/src/vcfentropy.cpp
+++ libvcflib/src/vcfentropy.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <getopt.h>
 #include "disorder.h"
 
--- libvcflib.orig/src/vcfevenregions.cpp
+++ libvcflib/src/vcfevenregions.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <getopt.h>
 #include <cmath>
 
--- libvcflib.orig/src/vcfgeno2haplo.cpp
+++ libvcflib/src/vcfgeno2haplo.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include "gpatInfo.hpp"
 #include <algorithm>
 #include <list>
--- libvcflib.orig/src/vcfinfosummarize.cpp
+++ libvcflib/src/vcfinfosummarize.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include "gpatInfo.hpp"
 #include <getopt.h>
 #include <algorithm>
--- libvcflib.orig/src/vcfintersect.cpp
+++ libvcflib/src/vcfintersect.cpp
@@ -11,7 +11,7 @@
 #include "BedReader.h"
 #include "IntervalTree.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <algorithm>
 #include <list>
 #include <set>
--- libvcflib.orig/src/vcfleftalign.cpp
+++ libvcflib/src/vcfleftalign.cpp
@@ -11,7 +11,7 @@
 #include "convert.h"
 #include "join.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <set>
 #include <vector>
 #include <getopt.h>
--- libvcflib.orig/src/vcfnormalizesvs.cpp
+++ libvcflib/src/vcfnormalizesvs.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 
 using namespace std;
 using namespace vcflib;
--- libvcflib.orig/src/vcfprimers.cpp
+++ libvcflib/src/vcfprimers.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <getopt.h>
 
 using namespace std;
--- libvcflib.orig/src/vcfremap.cpp
+++ libvcflib/src/vcfremap.cpp
@@ -11,7 +11,7 @@
 #include "BedReader.h"
 #include "IntervalTree.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <algorithm>
 #include <list>
 #include <set>
--- libvcflib.orig/src/vcfroc.cpp
+++ libvcflib/src/vcfroc.cpp
@@ -11,7 +11,7 @@
 #include "BedReader.h"
 #include "IntervalTree.h"
 #include <getopt.h>
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <algorithm>
 #include <list>
 #include <set>
--- libvcflib.orig/src/vcfsample2info.cpp
+++ libvcflib/src/vcfsample2info.cpp
@@ -9,7 +9,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include <getopt.h>
 #include <algorithm>
 #include <numeric>