1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
|
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";
|
