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
|
chimerauchimecommand.cpp | 2 +-
clearcutcommand.cpp | 32 ++++++++++++++++----------------
2 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index bd31c19..2070840 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
}
if (ucl) {
- char* tempucl = new char[5];
+ char* tempucl = new char[6];
strcpy(tempucl, "--ucl");
cPara.push_back(tempucl);
}
diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 6a0eb25..2e8164e 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -269,35 +269,35 @@ int ClearcutCommand::execute() {
vector<char*> cPara;
- char* tempClearcut = new char[8];
+ char* tempClearcut = new char[16];
strcpy(tempClearcut, "clearcut");
cPara.push_back(tempClearcut);
//you gave us a distance matrix
- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
+ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); }
//you gave us a fastafile
- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
+ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
+ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); }
+ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
+ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
if (seed != "*") {
string tempSeed = "--seed=" + seed;
char* temp = new char[tempSeed.length()];
strcpy(temp, tempSeed.c_str());
cPara.push_back(temp);
}
- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
+ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
+ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
+ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
string tempIn = "--in=" + inputFile;
char* tempI = new char[tempIn.length()];
strcpy(tempI, tempIn.c_str());
cPara.push_back(tempI);
- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
+ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
else{
string tempOut = "--out=" + outputName;
@@ -306,10 +306,10 @@ int ClearcutCommand::execute() {
cPara.push_back(temp);
}
- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
+ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
+ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); }
+ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
+ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
if (matrixout != "") {
string tempMatrix = "--matrixout=" + outputDir + matrixout;
char* temp = new char[tempMatrix.length()];
@@ -326,8 +326,8 @@ int ClearcutCommand::execute() {
cPara.push_back(temp);
}
- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
+ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
+ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
char** clearcutParameters;
clearcutParameters = new char*[cPara.size()];
|
