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
@@ -60,6 +60,7 @@
 pkg_check_modules(HTSLIB htslib)   # Optionally builds from contrib/
 pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/
 pkg_check_modules(SMITHWATERMAN REQUIRED IMPORTED_TARGET libsmithwaterman)
+pkg_check_modules(FASTAHACK REQUIRED IMPORTED_TARGET libfastahack)
 
 # ---- Build switches
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -109,7 +110,6 @@
 # ---- Include files
 
 include_directories(include)
-include_directories(contrib/fastahack)
 include_directories(contrib/intervaltree)
 # include_directories(contrib/multichoose) merged with vcflib
 include_directories(contrib/filevercmp)
@@ -146,7 +146,6 @@
   src/*.h*
   # contrib/multichoose/*.h*
   contrib/intervaltree/*.h*
-  contrib/fastahack/*.h*
   contrib/filevercmp/*.h*
   )
 
@@ -170,13 +169,13 @@
     src/LeftAlign.cpp
     src/cigar.cpp
     src/allele.cpp
-    contrib/fastahack/Fasta.cpp
     contrib/filevercmp/filevercmp.c
     contrib/c-progress-bar/progress.c
 )
 
 target_link_libraries(vcflib
     PkgConfig::SMITHWATERMAN
+    PkgConfig::FASTAHACK
     )
 
 if (TABIXPP_LOCAL) # add the tabixpp source file
--- 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
@@ -10,7 +10,7 @@
 
 #include "Variant.h"
 #include "split.h"
-#include "Fasta.h"
+#include <fastahack/Fasta.h>
 #include "gpatInfo.hpp"
 #include <getopt.h>
 #include <string.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
@@ -12,7 +12,7 @@
 #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>