Description: Use_shared_libs
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,7 +1,6 @@
-BAMTOOLS_ROOT = $(CURDIR)/bamtools
 CC = g++
-CFLAGS = -Wl,-rpath,$(BAMTOOLS_ROOT)/lib  -Wall -O3  -I $(BAMTOOLS_ROOT)/include -L $(BAMTOOLS_ROOT)/lib
-TABIX = tabix/tabix.o  -L./tabix -ltabix -lz
+CFLAGS = -Wall -O3  -I /usr/include/bamtools -I /usr/include
+TABIX = -ltabixpp -lhts -lz
 STATS_OBJS =  trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
 SCORE_OBJS = errorWindow.o utils.o histogram.o
 BREAK_OBJS = fasta.o utils.o
@@ -35,46 +34,46 @@
 	$(CC) $(CFLAGS) -c histogram.cpp
 
 utils.o: utils.cpp
-	$(CC) $(CFLAGS) -lbamtools -c utils.cpp
+	$(CC) $(CFLAGS) -c utils.cpp
 
 task_stats: task_stats.o $(STATS_OBJS)
-	$(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools -o task_stats $(TABIX)
+	$(CC) $(CFLAGS) task_stats.o  $(STATS_OBJS)  -lbamtools $(TABIX) -o task_stats
 
 task_stats.o: task_stats.cpp $(STATS_OBJS)
 	$(CC) $(CFLAGS) -c task_stats.cpp
 
 task_score: task_score.o $(SCORE_OBJS)
-	$(CC) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools -o task_score $(TABIX)
+	$(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX)
 
 task_score.o: task_score.cpp $(SCORE_OBJS)
 	$(CC) $(CFLAGS) -c task_score.cpp
 
 task_break: task_break.o $(BREAK_OBJS)
-	$(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools -o task_break $(TABIX)
+	$(CC) $(CFLAGS) task_break.o -lbamtools $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break
 
 task_break.o: task_break.cpp $(BREAK_OBJS)
 	$(CC) $(CFLAGS) -c task_break.cpp
 
 bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS)
-	$(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) -lbamtools -o bam2fragCov $(TABIX)
+	$(CC) $(CFLAGS) bam2fragCov.o -lbamtools $(BAM2COV_OBJS) -lbamtools $(TABIX) -o bam2fragCov
 
 bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS)
 	$(CC) $(CFLAGS) -c bam2fragCov.cpp
 
 bam2insert: bam2insert.o $(BAM2INSERT_OBJS)
-	$(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) -lbamtools -o bam2insert $(TABIX)
+	$(CC) $(CFLAGS) bam2insert.o -lbamtools $(BAM2INSERT_OBJS) -lbamtools $(TABIX) -o bam2insert
 
 bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS)
 	$(CC) $(CFLAGS) -c bam2insert.cpp
 
 bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS)
-	$(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) -lbamtools -o bam2perfect $(TABIX)
+	$(CC) $(CFLAGS) bam2perfect.o -lbamtools $(BAM2PERFECT_OBJS) -lbamtools $(TABIX) -o bam2perfect
 
 bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS)
 	$(CC) $(CFLAGS) -c bam2perfect.cpp
 
 bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
-	$(CC) $(CFLAGS) bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -lbamtools -o bam2fcdEstimate $(TABIX)
+	$(CC) $(CFLAGS) bam2fcdEstimate.o -lbamtools $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate
 
 bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
 	$(CC) $(CFLAGS) -c bam2fcdEstimate.cpp
@@ -110,13 +109,13 @@
 	$(CC) $(CFLAGS) -c scaff2contig.cpp
 
 task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
-	$(CC) $(CFLAGS) task_gapresize.o $(GAPRESIZE_OBJS) -lbamtools -o task_gapresize $(TABIX)
+	$(CC) $(CFLAGS) task_gapresize.o -lbamtools $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize
 
 task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
 	$(CC) $(CFLAGS) -c task_gapresize.cpp
 
 task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
-	$(CC) $(CFLAGS) task_fcdrate.o $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(TABIX)
+	$(CC) $(CFLAGS) task_fcdrate.o -lbamtools $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate
 
 task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
 	$(CC) $(CFLAGS) -c task_fcdrate.cpp
--- a/src/task_break.cpp
+++ b/src/task_break.cpp
@@ -10,7 +10,6 @@
 #include <assert.h>
 #include "fasta.h"
 #include "utils.h"
-#include "tabix/tabix.hpp"
 
 using namespace std;
 
--- a/src/task_score.cpp
+++ b/src/task_score.cpp
@@ -18,7 +18,6 @@
 #include "histogram.h"
 #include "api/BamMultiReader.h"
 #include "api/BamReader.h"
-#include "tabix/tabix.hpp"
 
 using namespace BamTools;
 using namespace std;
--- a/src/task_stats.cpp
+++ b/src/task_stats.cpp
@@ -18,7 +18,6 @@
 #include "utils.h"
 #include "api/BamMultiReader.h"
 #include "api/BamReader.h"
-#include "tabix/tabix.hpp"
 
 using namespace BamTools;
 using namespace std;
--- a/src/utils.h
+++ b/src/utils.h
@@ -11,7 +11,7 @@
 
 #include "api/BamMultiReader.h"
 #include "api/BamReader.h"
-#include "tabix/tabix.hpp"
+#include "tabix.hpp"
 
 const short INNIE = 1;
 const short OUTTIE = 2;
--- a/src/task_fcdrate.cpp
+++ b/src/task_fcdrate.cpp
@@ -9,7 +9,6 @@
 
 #include "utils.h"
 #include "histogram.h"
-#include "tabix/tabix.hpp"
 
 using namespace std;
 
--- a/src/reapr.pl
+++ b/src/reapr.pl
@@ -12,8 +12,8 @@
 $this_script = File::Spec->rel2abs($this_script);
 my ($scriptname, $scriptdir) = fileparse($this_script);
 $scriptdir = File::Spec->rel2abs($scriptdir);
-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+my $tabix = 'tabix';
+my $bgzip = 'bgzip';
 my $version = '1.0.18';
 
 if ($#ARGV == -1) {
--- a/src/task_preprocess.pl
+++ b/src/task_preprocess.pl
@@ -52,9 +52,9 @@
 my $ideal_fcd_file = File::Spec->catfile($sample_dir, 'ideal_fcd.txt');
 my $lowess_prefix = File::Spec->catfile($sample_dir, 'gc_vs_cov.lowess');
 my $r_script = File::Spec->catfile($sample_dir, 'gc_vs_cov.R');
-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+my $tabix = 'tabix';
+my $bgzip = 'bgzip';
+my $samtools = 'samtools';
 
 # make directory and soft links to required files
 $fasta_in = File::Spec->rel2abs($fasta_in);
--- a/src/task_perfectfrombam.pl
+++ b/src/task_perfectfrombam.pl
@@ -57,12 +57,12 @@
 my $min_perfect_map_qual = $ARGV[5];
 my $min_align_score = $ARGV[6];
 my $bam2perfect = File::Spec->catfile($scriptdir, 'bam2perfect');
-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+my $bgzip = 'bgzip';
+my $tabix = 'tabix';
 my $ERROR_PREFIX = '[REAPR perfectfrombam]';
 my $perfect_bam = "$out_prefix.tmp.perfect.bam";
 my $repetitive_bam = "$out_prefix.tmp.repetitive.bam";
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+my $samtools = 'samtools';
 my %seq_lengths;
 my %used_seqs;
 my $hist_file = "$out_prefix.hist";
--- a/src/task_perfectmap.pl
+++ b/src/task_perfectmap.pl
@@ -38,14 +38,14 @@
 my $reads_2 = $ARGV[2];
 my $fragsize = $ARGV[3];
 my $preout = $ARGV[4];
-my $findknownsnps = File::Spec->catfile($scriptdir, 'findknownsnps');
+my $findknownsnps = 'findknownsnps';
 my $ERROR_PREFIX = '[REAPR perfect_map]';
 my $raw_coverage_file = "$preout.tmp.cov.txt";
 my $tmp_bin = "$preout.tmp.bin";
 my $tmp_bin_single_match = "$tmp_bin\_single_match.fastq";
-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+my $tabix = 'tabix';
+my $bgzip = 'bgzip';
+my $samtools = 'samtools';
 my $all_bases_outfile = "$preout.perfect_cov.gz";
 my $hist_outfile = "$preout.hist";
 my @coverage = (0) x 101;
--- a/src/task_plots.pl
+++ b/src/task_plots.pl
@@ -50,9 +50,9 @@
 }
 
 
-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+my $tabix = 'tabix';
+my $bgzip = 'bgzip';
+my $samtools = 'samtools';
 my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f', 'read_ratio_r', 'clip', 'FCD_err');
 my @file_list;
 my $fa_out = "$outprefix.ref.fa";
--- a/src/task_pipeline.pl
+++ b/src/task_pipeline.pl
@@ -9,7 +9,7 @@
 
 my ($scriptname, $scriptdir) = fileparse($0);
 my $reapr_dir = abs_path(File::Spec->catfile($scriptdir, File::Spec->updir()));
-my $reapr = File::Spec->catfile($reapr_dir, 'reapr');
+my $reapr = 'reapr';
 
 my %options = (fcdcut => 0);
 
--- a/src/task_seqrename.pl
+++ b/src/task_seqrename.pl
@@ -7,7 +7,7 @@
 use Getopt::Long;
 
 my ($scriptname, $scriptdir) = fileparse($0);
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+my $samtools = 'samtools';
 my %options;
 my $usage = qq/<rename file> <in.bam> <out.bam>
 
--- a/src/task_smaltmap.pl
+++ b/src/task_smaltmap.pl
@@ -77,8 +77,8 @@
 my $reads_2 = $ARGV[2];
 my $final_bam = $ARGV[3];
 my $ERROR_PREFIX = '[REAPR smaltmap]';
-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
-my $smalt = File::Spec->catfile($scriptdir, 'smalt');
+my $samtools = 'samtools';
+my $smalt = 'smalt';
 my $tmp_prefix = "$final_bam.tmp.$$.smaltmap";
 my $smalt_index = "$tmp_prefix.smalt_index";
 my $smalt_sample = "$tmp_prefix.smalt_sample";
