Commit 7ea96146 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: '-u' results are now in '.affects' file

This was not a .fa file, and now it contains all reads.
parent f63fd911
!LAUNCH: ../../vidjil -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep not out2/Stanford_S22.unsegmented.fa
!LAUNCH: ../../vidjil -r 5 -o out2 -u -U -v -G ../../germline/IGH ../../data/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep not out2/Stanford_S22.affects
# Testing uncommon and debug options
$ verbose (-v)
......
......@@ -89,7 +89,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define CLONE_FILENAME "clone.fa-"
#define WINDOWS_FILENAME ".windows.fa"
#define SEGMENTED_FILENAME ".segmented.vdj.fa"
#define UNSEGMENTED_FILENAME ".unsegmented.fa"
#define AFFECTS_FILENAME ".affects"
#define EDGES_FILENAME ".edges"
#define COMP_FILENAME "comp.vidjil"
#define JSON_SUFFIX ".vidjil"
......@@ -203,8 +203,7 @@ void usage(char *progname)
<< "Debug" << endl
<< " -U output segmented (in " << SEGMENTED_FILENAME << " file) sequences" << endl
<< " -u output unsegmented (in " << UNSEGMENTED_FILENAME << " file) sequences" << endl
<< " and display detailed k-mer affectation both on segmented and on unsegmented sequences" << endl
<< " -u output detailed k-mer affectation both on segmented and on unsegmented sequences (in " << AFFECTS_FILENAME << " file)" << endl
<< "Output" << endl
<< " -o <dir> output directory (default: " << DEFAULT_OUT_DIR << ")" << endl
<< " -b <string> output basename (by default basename of the input file)" << endl
......@@ -854,7 +853,7 @@ int main (int argc, char **argv)
}
if (output_unsegmented) {
string f_unsegmented = out_dir + f_basename + UNSEGMENTED_FILENAME ;
string f_unsegmented = out_dir + f_basename + AFFECTS_FILENAME ;
cout << " ==> " << f_unsegmented << endl ;
out_unsegmented = new ofstream(f_unsegmented.c_str());
we.setUnsegmentedOutput(out_unsegmented);
......
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