char* get_last_word(char * str) {
char *res;
int i=0;
res = (char*)malloc(sizeof(char));
int l = leng(str);
l--;
while (str[l] == ' ' && l != 0)l--;
while (str[l] != ' ' && l != 0)l--;
while (str[l] != ' ' && str[l] != '\0')
res[i++] = str[l++];
res[i] = '\0';
return res;
}
void ParseSNP::parse_cmd_line(int argc, char *argv[]) {
CmdLine cmdss("computes local coverage and a derived BOD quality score", ' ', version.c_str());
ValueArg<string> read_filename_arg("q", "mapped_reads",
"Mapped read file (sam/bam)", true, "#", "string");
cmdss.add(read_filename_arg);
//
ValueArg<string> ref_file_arg("r", "ref_file", "Reference file (fasta)", true, "#", "string");
cmdss.add(ref_file_arg);
//
ValueArg<string> snp_file_arg("s", "snp_file", "VCF file", true, "#", "string");
cmdss.add(snp_file_arg);
//
ValueArg<int> leng("l", "read_length", "maximum read length", true, -1, "int");
cmdss.add(leng);
//
ValueArg<string> db_file_arg("d", "db_file", "Sqlite file to write the output", false, "#", "string");
//
ValueArg<string> plot_file_arg("p", "plot_file",
"Name of the file for the data required for the Python script",
false, "#", "string");
//
cmdss.xorAdd( db_file_arg, plot_file_arg ); // <- whether Sqlite DB or plain text
//
ValueArg<string> sample_label_arg("t", "sample_label",
"sample label for the database",
false, "#", "string");
cmdss.add(sample_label_arg);
//
MultiArg<string> exclude_contigs_arg("x", "exclude", "exclude contigs from analysis", false, "string");
cmdss.add(exclude_contigs_arg);
//
MultiSwitchArg verbose_arg("v", "verbose", "print snp-by-snp progress", 0);
cmdss.add(verbose_arg);
//
ValueArg<int> num_test_arg("b", "break_after", "max number of position per chromosome [test mode]", false, 0, "int");
cmdss.add(num_test_arg);
try {
cmdss.parse(argc, argv); //parse arguments
read_filename = read_filename_arg.getValue();
/* output = out.getValue();
if (output[0] == '#') {
output = read_filename;
output += ".mot";
}
*/
reffile = ref_file_arg.getValue();
snpfile = snp_file_arg.getValue();
read_length = leng.getValue();
range = 3 * read_length / 2 ;
if ( plot_file_arg.isSet() )
plot_file = plot_file_arg.getValue();
//db_file = '#';
else if ( db_file_arg.isSet() )
// plot_file = '#';
plot_file = db_file_arg.getValue();
//
if ( sample_label_arg.isSet() )
sample_label = sample_label_arg.getValue();
else
sample_label = "[" + db_file_arg.getValue() + "]";
clog << "table base name: " << sample_label << endl;
exclude_contigs = exclude_contigs_arg.getValue();
verbose = verbose_arg.getValue();
if (verbose){
num_test = num_test_arg.getValue();
}
//
db_flag = db_file_arg.isSet();
init();
parseVCF();
} catch (ArgException &e) {
StdOutput out;
out.failure(cmdss, e);
}
}
