From 25d3e40636afd9eac73a1d455be7eeac68e991a4 Mon Sep 17 00:00:00 2001
From: Terence Li <terence@usc.edu>
Date: Thu, 15 Oct 2020 16:07:38 -0700
Subject: [PATCH] removed extraneous #include for hts support. updated version
 number. added dependencies in Makefile so that users who clone can compile
 with htslib support

---
 src/Makefile                     | 3 ++-
 src/load_data_for_complexity.cpp | 1 -
 src/preseq.cpp                   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index eabf4d7..d47ddf8 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -42,7 +42,8 @@ $(PROGS): $(addprefix smithlab_cpp/, \
 	OptionParser.o MappedRead.o)
 
 ifdef HAVE_HTSLIB
-preseq to-mr: $(addprefix smithlab_cpp/, htslib_wrapper.o)
+preseq to-mr: $(addprefix smithlab_cpp/, \
+  htslib_wrapper_deprecated.o cigar_utils.o)
 endif
 
 preseq: continued_fraction.o load_data_for_complexity.o moment_sequence.o
diff --git a/src/load_data_for_complexity.cpp b/src/load_data_for_complexity.cpp
index 24acdbb..bef5102 100644
--- a/src/load_data_for_complexity.cpp
+++ b/src/load_data_for_complexity.cpp
@@ -181,7 +181,6 @@ empty_pq(GenomicRegion &curr_gr, GenomicRegion &prev_gr,
  */
 #ifdef HAVE_HTSLIB
 // switching dependency on bamtools to samtools
-#include <htslib_wrapper.hpp>
 #include "htslib_wrapper_deprecated.hpp"
 
 size_t
diff --git a/src/preseq.cpp b/src/preseq.cpp
index 80c21ab..7de42ba 100644
--- a/src/preseq.cpp
+++ b/src/preseq.cpp
@@ -56,7 +56,7 @@ using std::to_string;
 using std::mt19937;
 using std::max;
 
-static const string preseq_version = "3.0.2";
+static const string preseq_version = "3.1.1";
 
 template <typename T> T
 get_counts_from_hist(const vector<T> &h) {