Commit da0a38e5 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: update help strings

parent e34aa009
......@@ -485,7 +485,7 @@ int main (int argc, char **argv)
double expected_value = THRESHOLD_NB_EXPECTED;
app.add_option("--e-value,-e", expected_value,
"maximal e-value for determining if a V-J segmentation can be trusted", true)
"maximal e-value for trusting the detection of a V-J recombination", true)
-> group(group) -> transform(string_NO_LIMIT);
Cost segment_cost = DEFAULT_SEGMENT_COST ;
......@@ -499,7 +499,7 @@ int main (int argc, char **argv)
double expected_value_D = THRESHOLD_NB_EXPECTED_D;
app.add_option("--analysis-e-value-D,-E", expected_value_D,
"maximal e-value for determining if a D segment can be trusted", true)
"maximal e-value for trusting the detection of a D segment", true)
-> group(group) -> level();
int kmer_threshold = DEFAULT_KMER_THRESHOLD;
......@@ -548,7 +548,7 @@ int main (int argc, char **argv)
bool output_segmented = false;
app.add_flag("--out-analyzed,-U", output_segmented,
"output analyzed reads (in " SEGMENTED_FILENAME " file)")
"output reads with detected recombinations (in " SEGMENTED_FILENAME " file)")
-> group(group);
bool output_unsegmented = false;
......@@ -560,9 +560,9 @@ int main (int argc, char **argv)
output_unsegmented_detail_full = (n >= 2); // -uu
output_unsegmented_detail = (n >= 1); // -u
}, R"Z(
-u output unanalyzed reads, gathered by cause, except for very short and 'too few V/J' reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files)
-uu output unanalyzed reads, gathered by cause, all reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files) (use only for debug)
-uuu output unanalyzed reads, all reads, including a )Z" UNSEGMENTED_FILENAME R"Z( file (use only for debug))Z")
-u output undetected reads, gathered by cause, except for very short and 'too few V/J' reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files)
-uu output undetected reads, gathered by cause, all reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files) (use only for debug)
-uuu output undetected reads, all reads, including a )Z" UNSEGMENTED_FILENAME R"Z( file (use only for debug))Z")
-> group(group);
bool output_sequences_by_cluster = false;
......
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