Commit 4ab03c22 authored by Mathieu Giraud's avatar Mathieu Giraud

tests, vidjil.cpp: --ratio instead of -%

See #2739.
parent 025efba7
!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log && $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH -% 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log && diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22.log
!LAUNCH: $LAUNCHER $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -z 1 -k 9 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH --ratio 0.001 -r 2 -x 1000 -y 1 -c clones $VIDJIL_DATA/Stanford_S22.rc.fasta | sed 's/--IGH--.*VDJ\\(.*\\).$/\\1/' | sed 's/IGH SEG_./IGH SEG_X/' > vidjil_s22_rc.log
!LAUNCH: diff out/Stanford_S22{,.rc}.vidjil | grep GGG && diff vidjil_s22.log vidjil_s22_rc.log
!EXIT_CODE: 1
$ Same number segmented
......
......@@ -400,7 +400,7 @@ int main (int argc, char **argv)
group = "Labeled sequences (windows related to these sequences will be kept even if -r/-% thresholds are not reached)";
group = "Labeled sequences (windows related to these sequences will be kept even if -r/--ratio thresholds are not reached)";
app.add_option("-W", windows_labels_explicit, "label the given sequence") -> group(group);
......@@ -472,7 +472,7 @@ int main (int argc, char **argv)
max_representatives = NO_LIMIT_VALUE ;
max_clones = NO_LIMIT_VALUE ;
},
"reports and segments all clones (-r 0 -% 0 -y " NO_LIMIT " -z " NO_LIMIT "), to be used only on very small datasets (for example -AX 20)") -> group(group);
"reports and segments all clones (-r 0 --ratio 0 -y " NO_LIMIT " -z " NO_LIMIT "), to be used only on very small datasets (for example -AX 20)") -> group(group);
app.add_option("-x", max_reads_processed_sample,
"maximal number of reads to process ('" NO_LIMIT "': no limit, default), only first reads") -> group(group) -> transform(string_NO_LIMIT);
......@@ -1136,7 +1136,7 @@ int main (int argc, char **argv)
if (sort_clones.size() == 0)
{
cout << " ! No clones with current parameters." << endl;
cout << " ! See the 'Limits to report a clone' options (-r, -%, -z, -A)." << endl;
cout << " ! See the 'Limits to report a clone' options (-r, --ratio, -z, -A)." << endl;
}
else
{
......
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