Commit 1d5ebc17 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: takes, by default, homo-sapiens.germlines

See #1987.
parent 55f4a8d5
...@@ -69,7 +69,7 @@ ...@@ -69,7 +69,7 @@
//$$ #define (mainly default options) //$$ #define (mainly default options)
#define DEFAULT_MULTI_GERMLINE_PATH "germline/" #define DEFAULT_MULTI_GERMLINE_PATH "germline/"
#define DEFAULT_MULTI_GERMLINE_FILE "germlines.data" #define DEFAULT_MULTI_GERMLINE_FILE "homo-sapiens.germlines"
#define DEFAULT_READ_HEADER_SEPARATOR " " #define DEFAULT_READ_HEADER_SEPARATOR " "
#define DEFAULT_READS "./data/Stanford_S22.fasta" #define DEFAULT_READS "./data/Stanford_S22.fasta"
...@@ -163,9 +163,9 @@ void usage(char *progname, bool advanced) ...@@ -163,9 +163,9 @@ void usage(char *progname, bool advanced)
<< " -D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components" << endl << " -D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components" << endl
<< " -J <file> J germline multi-fasta file" << endl << " -J <file> J germline multi-fasta file" << endl
<< " -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)" << endl << " -G <prefix> prefix for V (D) and J repertoires (shortcut for -V <prefix>V.fa -D <prefix>D.fa -J <prefix>J.fa) (basename gives germline code)" << endl
<< " -g <path> multiple locus/germlines. In the path <path>, takes 'germlines.data' to select locus and parameters" << endl << " -g <path> multiple locus/germlines. In the path <path>, takes '" << DEFAULT_MULTI_GERMLINE_FILE << "' to select locus and parameters" << endl
<< " Selecting '-g germline' processes TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl << " Selecting '-g germline' processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl
<< " A different 'germlines.data' file can also be provided with -g <file>" << endl << " Files different than '" << DEFAULT_MULTI_GERMLINE_FILE << "', for example for other species, can also be provided with -g <file>" << endl
<< endl << endl
<< "Locus/recombinations" << endl << "Locus/recombinations" << endl
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment