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--- a/src/KmerIndex.cpp
+++ b/src/KmerIndex.cpp
@@ -4,7 +4,7 @@
#include <ctype.h>
#include <zlib.h>
#include <unordered_set>
-#include "kseq.h"
+#include <htslib/kseq.h>
#ifndef KSEQ_INIT_READY
#define KSEQ_INIT_READY
--- a/src/ProcessReads.cpp
+++ b/src/ProcessReads.cpp
@@ -1,6 +1,6 @@
/*
#include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
#include <string>
#include <vector>
#include <unordered_map>
@@ -20,7 +20,7 @@
#include <iomanip>
#include "ProcessReads.h"
-#include "kseq.h"
+#include <htslib/kseq.h>
#include "PseudoBam.h"
#include "Fusion.hpp"
#include "BUSData.h"
--- a/src/ProcessReads.h
+++ b/src/ProcessReads.h
@@ -2,7 +2,7 @@
#define KALLISTO_PROCESSREADS_H
#include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
#include <string>
#include <vector>
#include <unordered_map>
--- a/unit_tests/test_kmerhashtable.cpp
+++ b/unit_tests/test_kmerhashtable.cpp
@@ -13,7 +13,7 @@
#include "KmerHashTable.h"
#include <zlib.h>
-#include "kseq.h"
+#include <htslib/kseq.h>
#ifndef KSEQ_INIT_READY
#define KSEQ_INIT_READY
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