Commit 3251bf81 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: -c germlines, init

We want to have a command that browse a set of reads and predict the germlines used.
(Perhaps, in the future, some results of this scenario could be used as an input of the segment scenario ?)
parent 6b41ea05
......@@ -73,8 +73,9 @@
#define COMMAND_WINDOWS "windows"
#define COMMAND_ANALYSIS "clones"
#define COMMAND_SEGMENT "segment"
#define COMMAND_GERMLINES "germlines"
enum { CMD_WINDOWS, CMD_ANALYSIS, CMD_SEGMENT } ;
enum { CMD_WINDOWS, CMD_ANALYSIS, CMD_SEGMENT, CMD_GERMLINES } ;
#define OUT_DIR "./out/"
#define CLONES_FILENAME "clones.vdj.fa"
......@@ -135,6 +136,7 @@ void usage(char *progname)
<< " -c <command> \t" << COMMAND_WINDOWS << "\t window extracting (default)" << endl
<< " \t\t" << COMMAND_ANALYSIS << " \t clone analysis" << endl
<< " \t\t" << COMMAND_SEGMENT << " \t V(D)J segmentation (not recommended)" << endl
<< " \t\t" << COMMAND_GERMLINES << " \t discover all germlines" << endl
<< endl
<< "Germline databases" << endl
......@@ -205,6 +207,7 @@ void usage(char *progname)
<< " " << progname << " -G germline/IGH -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c clones -G germline/IGH -r 5 -R 5 -d data/Stanford_S22.fasta" << endl
<< " " << progname << " -c segment -G germline/IGH -d data/Stanford_S22.fasta # (only for testing)" << endl
<< " " << progname << " -c germlines data/Stanford_S22.fasta" << endl
;
exit(1);
}
......@@ -310,6 +313,8 @@ int main (int argc, char **argv)
command = CMD_SEGMENT;
else if (!strcmp(COMMAND_WINDOWS,optarg))
command = CMD_WINDOWS;
else if (!strcmp(COMMAND_GERMLINES,optarg))
command = CMD_GERMLINES;
else {
cerr << "Unknwown command " << optarg << endl;
usage(argv[0]);
......@@ -534,6 +539,8 @@ int main (int argc, char **argv)
break;
case CMD_SEGMENT: cout << "Segmenting V(D)J" << endl;
break;
case CMD_GERMLINES: cout << "Discovering germlines" << endl;
break;
}
cout << "Command line: ";
......@@ -566,6 +573,17 @@ int main (int argc, char **argv)
cout << endl ;
#endif
//////////////////////////////://////////
// DISCOVER GERMLINES //
/////////////////////////////////////////
if (command == CMD_GERMLINES)
{
exit(0);
}
//////////////////////////////////
//$$ Read sequence files
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment