Commit 47b30c75 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: example data is now in 'demo/'

See #2611.
parent 6b110757
......@@ -74,7 +74,7 @@
#define DEFAULT_MULTI_GERMLINE_FILE "homo-sapiens.g"
#define DEFAULT_READ_HEADER_SEPARATOR " "
#define DEFAULT_READS "./data/Stanford_S22.fasta"
#define DEFAULT_READS "./demo/Stanford_S22.fasta"
#define DEFAULT_MIN_READS_CLONE 5
#define DEFAULT_MAX_REPRESENTATIVES 100
#define DEFAULT_MAX_CLONES 100
......@@ -102,8 +102,6 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define COMP_FILENAME "comp.vidjil"
#define JSON_SUFFIX ".vidjil"
// "tests/data/leukemia.fa"
#define DEFAULT_K 0
#define DEFAULT_W 50
#define DEFAULT_SEED DEFAULT_GERMLINE_SEED
......@@ -260,12 +258,12 @@ void usage(char *progname, bool advanced)
<< endl
<< "Examples (see doc/algo.org)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 data/Stanford_S22.fasta # (basic usage, detect the locus for each read," << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g -2 -3 demo/Stanford_S22.fasta # (basic usage, detect the locus for each read," << endl
<< " # including unexpected recombinations, analyzes CDR3)" << endl
<< " " << progname << " -c clones -g germline/homo-sapiens.g:IGH -3 data/Stanford_S22.fasta # (restrict to complete recombinations on the IGH locus)" << endl
<< " " << progname << " -c windows -g germline/homo-sapiens.g -2 -uu -U data/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 -X 50 data/Stanford_S22.fasta # (full analysis of each read, only for debug/testing, here on first 50 reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g data/Stanford_S22.fasta # (statistics on the k-mers)" << 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 windows -g germline/homo-sapiens.g -2 -uu -U demo/Stanford_S22.fasta # (detect the locus, splits all the reads into large files)" << endl
<< " " << progname << " -c segment -g germline/homo-sapiens.g -2 -3 -X 50 demo/Stanford_S22.fasta # (full analysis of each read, only for debug/testing, here on first 50 reads)" << endl
<< " " << progname << " -c germlines -g germline/homo-sapiens.g demo/Stanford_S22.fasta # (statistics on the k-mers)" << endl
;
exit(1);
}
......
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