test

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 0c8c2dd5d35e4fe54d1a705b1874fe2c78594fb5..99893a92e841ee92e7cee26910f0a5d3f973e840 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -9,6 +9,7 @@
 /* Begin PBXBuildFile section */
                219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
                219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
+               7E16B6F51695CB5C00C0DC4F /* main.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E16B6F41695CB5C00C0DC4F /* main.cpp */; };
                7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
                834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */; };
                834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */; };
@@ -385,6 +386,8 @@
                219C1DE11552C508004209F9 /* newcommandtemplate.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = newcommandtemplate.h; sourceTree = "<group>"; };
                219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
                219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
+               7E16B6F31695CB5C00C0DC4F /* pdsMakeContigs.1 */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text.man; name = pdsMakeContigs.1; path = pdsMakeContigs/pdsMakeContigs/pdsMakeContigs.1; sourceTree = "<group>"; };
+               7E16B6F41695CB5C00C0DC4F /* main.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = main.cpp; path = pdsMakeContigs/pdsMakeContigs/main.cpp; sourceTree = "<group>"; };
                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
@@ -1187,6 +1190,8 @@
                                A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
                                7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
                                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
+                               7E16B6F31695CB5C00C0DC4F /* pdsMakeContigs.1 */,
+                               7E16B6F41695CB5C00C0DC4F /* main.cpp */,
                                A77410F514697C300098E6AC /* seqnoise.h */,
                                A77410F414697C300098E6AC /* seqnoise.cpp */,
                                A7E9BA5312D39A5E00DA6239 /* read */,
@@ -2304,6 +2309,7 @@
                                834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */,
                                834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */,
                                A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
+                               7E16B6F51695CB5C00C0DC4F /* main.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };

diff --git a/pdsMakeContigs/pdsMakeContigs/main.cpp b/pdsMakeContigs/pdsMakeContigs/main.cpp
new file mode 100644 (file)
index 0000000..f467955
--- /dev/null
+++ b/pdsMakeContigs/pdsMakeContigs/main.cpp
@@ -0,0 +1,18 @@
+//
+//  main.cpp
+//  pdsMakeContigs
+//
+//  Created by Patrick Schloss on 1/2/13.
+//  Copyright (c) 2013 University of Michigan. All rights reserved.
+//
+
+#include <iostream>
+
+int main (int argc, const char * argv[])
+{
+
+    // insert code here...
+    std::cout << "Hello, World!\n";
+    return 0;
+}
+

diff --git a/pdsMakeContigs/pdsMakeContigs/pdsMakeContigs.1 b/pdsMakeContigs/pdsMakeContigs/pdsMakeContigs.1
new file mode 100644 (file)
index 0000000..d07499e
--- /dev/null
+++ b/pdsMakeContigs/pdsMakeContigs/pdsMakeContigs.1
@@ -0,0 +1,79 @@
+.\"Modified from man(1) of FreeBSD, the NetBSD mdoc.template, and mdoc.samples.\r
+.\"See Also:\r
+.\"man mdoc.samples for a complete listing of options\r
+.\"man mdoc for the short list of editing options\r
+.\"/usr/share/misc/mdoc.template\r
+.Dd 1/2/13               \" DATE \r
+.Dt pdsMakeContigs 1      \" Program name and manual section number \r
+.Os Darwin\r
+.Sh NAME                 \" Section Header - required - don't modify \r
+.Nm pdsMakeContigs,\r
+.\" The following lines are read in generating the apropos(man -k) database. Use only key\r
+.\" words here as the database is built based on the words here and in the .ND line. \r
+.Nm Other_name_for_same_program(),\r
+.Nm Yet another name for the same program.\r
+.\" Use .Nm macro to designate other names for the documented program.\r
+.Nd This line parsed for whatis database.\r
+.Sh SYNOPSIS             \" Section Header - required - don't modify\r
+.Nm\r
+.Op Fl abcd              \" [-abcd]\r
+.Op Fl a Ar path         \" [-a path] \r
+.Op Ar file              \" [file]\r
+.Op Ar                   \" [file ...]\r
+.Ar arg0                 \" Underlined argument - use .Ar anywhere to underline\r
+arg2 ...                 \" Arguments\r
+.Sh DESCRIPTION          \" Section Header - required - don't modify\r
+Use the .Nm macro to refer to your program throughout the man page like such:\r
+.Nm\r
+Underlining is accomplished with the .Ar macro like this:\r
+.Ar underlined text .\r
+.Pp                      \" Inserts a space\r
+A list of items with descriptions:\r
+.Bl -tag -width -indent  \" Begins a tagged list \r
+.It item a               \" Each item preceded by .It macro\r
+Description of item a\r
+.It item b\r
+Description of item b\r
+.El                      \" Ends the list\r
+.Pp\r
+A list of flags and their descriptions:\r
+.Bl -tag -width -indent  \" Differs from above in tag removed \r
+.It Fl a                 \"-a flag as a list item\r
+Description of -a flag\r
+.It Fl b\r
+Description of -b flag\r
+.El                      \" Ends the list\r
+.Pp\r
+.\" .Sh ENVIRONMENT      \" May not be needed\r
+.\" .Bl -tag -width "ENV_VAR_1" -indent \" ENV_VAR_1 is width of the string ENV_VAR_1\r
+.\" .It Ev ENV_VAR_1\r
+.\" Description of ENV_VAR_1\r
+.\" .It Ev ENV_VAR_2\r
+.\" Description of ENV_VAR_2\r
+.\" .El                      \r
+.Sh FILES                \" File used or created by the topic of the man page\r
+.Bl -tag -width "/Users/joeuser/Library/really_long_file_name" -compact\r
+.It Pa /usr/share/file_name\r
+FILE_1 description\r
+.It Pa /Users/joeuser/Library/really_long_file_name\r
+FILE_2 description\r
+.El                      \" Ends the list\r
+.\" .Sh DIAGNOSTICS       \" May not be needed\r
+.\" .Bl -diag\r
+.\" .It Diagnostic Tag\r
+.\" Diagnostic informtion here.\r
+.\" .It Diagnostic Tag\r
+.\" Diagnostic informtion here.\r
+.\" .El\r
+.Sh SEE ALSO \r
+.\" List links in ascending order by section, alphabetically within a section.\r
+.\" Please do not reference files that do not exist without filing a bug report\r
+.Xr a 1 , \r
+.Xr b 1 ,\r
+.Xr c 1 ,\r
+.Xr a 2 ,\r
+.Xr b 2 ,\r
+.Xr a 3 ,\r
+.Xr b 3 \r
+.\" .Sh BUGS              \" Document known, unremedied bugs \r
+.\" .Sh HISTORY           \" Document history if command behaves in a unique manner
\ No newline at end of file