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vidjil
vidjil
Commits
1d5ebc17
Commit
1d5ebc17
authored
Jan 25, 2017
by
Mathieu Giraud
Browse files
vidjil.cpp: takes, by default, homo-sapiens.germlines
See
#1987
.
parent
55f4a8d5
Changes
1
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Side-by-side
algo/vidjil.cpp
View file @
1d5ebc17
...
...
@@ -69,7 +69,7 @@
//$$ #define (mainly default options)
#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_READS "./data/Stanford_S22.fasta"
...
...
@@ -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
<<
" -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 <path> multiple locus/germlines. In the path <path>, takes '
germlines.data
' 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
<<
"
A
different
'germlines.data' file
can also be provided with -g <file>"
<<
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
human
TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations"
<<
endl
<<
"
Files
different
than '"
<<
DEFAULT_MULTI_GERMLINE_FILE
<<
"', for example for other species,
can also be provided with -g <file>"
<<
endl
<<
endl
<<
"Locus/recombinations"
<<
endl
...
...
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