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Commit 83a701e8 authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: preset --filter-reads

see #4681
parent 650c3ff3
......@@ -134,6 +134,10 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define MAX_CLONES_FOR_SIMILARITY 20
#define EVALUE_FILTER_READS 1e6
#define STR_(X) #X
#define STR(X) STR_(X)
// warn
#define WARN_MAX_CLONES 5000
#define WARN_PERCENT_SEGMENTED 40
......@@ -166,6 +170,7 @@ string usage_examples(char *progname)
<< " # including unexpected recombinations (-2), assign V(D)J genes and try to detect the CDR3s (-3))" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 demo/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 -z 20 demo/LIL-L4.fastq.gz # (basic usage, output detailed V(D)J analysis on the first 20 clones)" << endl
<< " " << progname << " --filter-reads -g germline/homo-sapiens.g demo/LIL-L4.fastq.gz # (pre-filter, extract all reads that may have V(D)J recombinations)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -y 0 -uu -U demo/LIL-L4.fastq.gz # (splits all the reads into (large) files depending on the detection of V(D)J recombinations)" << endl
<< " " << progname << " -c designations -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, here on 50 sampled reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g demo/Stanford_S22.fasta # (statistics on the k-mers)" << endl
......@@ -624,6 +629,20 @@ int main (int argc, char **argv)
// ----------------------------------------------------------------------------------------------------------------------
group = "Presets";
app.add_flag_function("--filter-reads", [&](int n) {
UNUSED(n);
cmd = COMMAND_WINDOWS;
output_segmented = true;
expected_value = EVALUE_FILTER_READS ;
multi_germline_unexpected_recombinations_12 = true;
max_representatives = 0;
max_clones = 0;
return true;
},
"filter possibly huge datasets, with a permissive threshold, to extract reads that may have V(D)J recombinations"
PAD_HELP "(equivalent to -c " COMMAND_WINDOWS " --out-detected --e-value " STR(EVALUE_FILTER_READS) " -2 --max-consensus 0)")
-> group(group);
app.add_option("--grep-reads",
[&only_labeled_windows,&windows_labels_explicit,&output_sequences_by_cluster](CLI::results_t res) {
only_labeled_windows = true;
......
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