Commit d9ec1f01 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp, tests: --header-sep

See #2739.
parent 4ab03c22
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS -\# FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
!LAUNCH: $VIDJIL_DIR/$EXEC $VIDJIL_DEFAULT_OPTIONS --header-sep FA -k 16 -z 0 -w 60 -r 5 -o out2 -uuu -U -v -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa $VIDJIL_DATA/Stanford_S22.fasta ; tail out2/Stanford_S22.segmented.vdj.fa ; grep UNSEG out2/Stanford_S22.unsegmented.vdj.fa
# Testing uncommon and debug options
$ verbose (-v)
......
......@@ -319,7 +319,7 @@ int main (int argc, char **argv)
-> group(group) -> set_type_name("COMMAND");
group = "Input" ;
app.add_option("--separator", read_header_separator, "separator for headers in the reads file", true) -> group(group) -> level() -> set_type_name("CHAR") ;
app.add_option("--header-sep", read_header_separator, "separator for headers in the reads file", true) -> group(group) -> level() -> set_type_name("CHAR") ;
group = "Germline presets (at least one -g or -V/(-D)/-J option must be given for all commands except -c " COMMAND_GERMLINES ")";
......
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