From 3cb8366e8b97f4ce35a920a87fdc775f95a11ff6 Mon Sep 17 00:00:00 2001
From: Matus Kosut <matus.kosut@ntnu.no>
Date: Wed, 28 Oct 2020 19:11:49 +0100
Subject: [PATCH 2/2] fix paths of imported libs - should never use path

---
 src/SAIGE_GENE_readDosageMatrix_vcf.cpp | 6 +++---
 src/SAIGE_readDosage_bgen.cpp           | 6 +++---
 src/SAIGE_readDosage_vcf.cpp            | 6 +++---
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/SAIGE_GENE_readDosageMatrix_vcf.cpp b/src/SAIGE_GENE_readDosageMatrix_vcf.cpp
index 3fe2fe267..3c684828f 100644
--- a/src/SAIGE_GENE_readDosageMatrix_vcf.cpp
+++ b/src/SAIGE_GENE_readDosageMatrix_vcf.cpp
@@ -1,6 +1,6 @@
-#include "../thirdParty/cget/include/savvy/reader.hpp"
-#include "../thirdParty/cget/include/savvy/region.hpp"
-#include "../thirdParty/cget/include/savvy/variant_group_iterator.hpp"
+#include <savvy/reader.hpp>
+#include <savvy/region.hpp>
+#include <savvy/variant_group_iterator.hpp>
 
 #include <iostream>
 #include <fstream>
diff --git a/src/SAIGE_readDosage_bgen.cpp b/src/SAIGE_readDosage_bgen.cpp
index f9f32d623..3881f88f3 100644
--- a/src/SAIGE_readDosage_bgen.cpp
+++ b/src/SAIGE_readDosage_bgen.cpp
@@ -3,9 +3,9 @@
 #include <cassert>
 #include <stdexcept>
 #include <memory>
-#include "../thirdParty/bgen/genfile/include/genfile/bgen/bgen.hpp"
-#include "../thirdParty/bgen/genfile/include/genfile/bgen/View.hpp"
-#include "../thirdParty/bgen/genfile/include/genfile/bgen/IndexQuery.hpp"
+#include <genfile/bgen/bgen.hpp>
+#include <genfile/bgen/View.hpp>
+#include <genfile/bgen/IndexQuery.hpp>
 #include <sstream>
 #include <time.h>
 #include <Rcpp.h>
diff --git a/src/SAIGE_readDosage_vcf.cpp b/src/SAIGE_readDosage_vcf.cpp
index 1b63c835a..a046c7978 100644
--- a/src/SAIGE_readDosage_vcf.cpp
+++ b/src/SAIGE_readDosage_vcf.cpp
@@ -1,6 +1,6 @@
-#include "../thirdParty/cget/include/savvy/reader.hpp"
-#include "../thirdParty/cget/include/savvy/varint.hpp"
-#include "../thirdParty/cget/include/savvy/sav_reader.hpp"
+#include <savvy/reader.hpp>
+#include <savvy/varint.hpp>
+#include <savvy/sav_reader.hpp>
 
 #include <iostream>
 #include <fstream>
-- 
2.23.0

