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Commit ddc2c454 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: remove out/sequences.fa-*, detailed output is in out/clone.fa-*

Clean the code, reorganizing output files
parent 94bd4c45
......@@ -84,7 +84,6 @@ enum { CMD_WINDOWS, CMD_ANALYSIS, CMD_SEGMENT, CMD_GERMLINES } ;
#define CLONES_FILENAME "clones.vdj.fa"
#define CLONE_FILENAME "clone.fa-"
#define WINDOWS_FILENAME "windows.fa"
#define SEQUENCES_FILENAME "sequences.fa"
#define SEGMENTED_FILENAME "segmented.vdj.fa"
#define UNSEGMENTED_FILENAME "unsegmented.fa"
#define EDGES_FILENAME "edges"
......@@ -203,7 +202,7 @@ void usage(char *progname)
<< " -o <dir> output directory (default: " << OUT_DIR << ")" << endl
<< " -p <string> prefix output filenames by the specified string" << endl
<< " -a output all sequences by cluster (" << SEQUENCES_FILENAME << "), to be used only on small datasets" << endl
<< " -a output all sequences by cluster (" << CLONE_FILENAME << "*), to be used only on small datasets" << endl
<< " -x do not compute representative sequences" << endl
<< " -v verbose mode" << endl
<< endl
......@@ -1028,15 +1027,9 @@ int main (int argc, char **argv)
string clone_file_name = out_seqdir+ prefix_filename + CLONE_FILENAME + string_of_int(num_clone) ;
string windows_file_name = out_seqdir+ prefix_filename + WINDOWS_FILENAME + "-" + string_of_int(num_clone) ;
string sequences_file_name = out_seqdir+ prefix_filename + SEQUENCES_FILENAME + "-" + string_of_int(num_clone) ;
ofstream out_clone(clone_file_name.c_str());
ofstream out_windows(windows_file_name.c_str());
ofstream out_sequences;
if (output_sequences_by_cluster) {
out_sequences.open(sequences_file_name.c_str());
}
cout << "Clone #" << right << setfill('0') << setw(WIDTH_NB_CLONES) << num_clone ;
cout << " – " << setfill(' ') << setw(WIDTH_NB_READS) << clone_nb_reads << " reads" ;
......@@ -1116,19 +1109,14 @@ int main (int argc, char **argv)
representative.label = string_of_int(it->second) + "--" + representative.label;
if (output_sequences_by_cluster) // -a option, output all sequences
{
out_sequences << ">" << it->second << "--window--" << num_seq << " " << windows_labels[it->first] << endl ;
out_sequences << it->first << endl;
if (representative != NULL_SEQUENCE)
out_sequences << representative ;
list<Sequence> &sequences = windowsStorage->getReads(it->first);
for (list<Sequence>::const_iterator itt = sequences.begin(); itt != sequences.end(); ++itt)
{
out_sequences << *itt ;
out_clone << *itt ;
}
}
......
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