Commit 6226ac4a authored by Mathieu Giraud's avatar Mathieu Giraud

germline/: rename to homo-sapiens.g

The .g files will be now referred as "germline/homo-sapiens.g", instead of
the longer and redundant "germline/homo-sapiens.germline".
This will improve readability at several places, and is
far more meaningful than the previous "germline/germlines.data".
parent 8a7a3c83
......@@ -69,7 +69,7 @@
//$$ #define (mainly default options)
#define DEFAULT_MULTI_GERMLINE_PATH "germline/"
#define DEFAULT_MULTI_GERMLINE_FILE "homo-sapiens.germlines"
#define DEFAULT_MULTI_GERMLINE_FILE "homo-sapiens.g"
#define DEFAULT_READ_HEADER_SEPARATOR " "
#define DEFAULT_READS "./data/Stanford_S22.fasta"
......
......@@ -228,9 +228,9 @@ Germline databases (at least one -V/(-D)/-J, or -G, or -g option must be given f
-D <file> D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components
-J <file> J germline multi-fasta file
-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)
-g <path> multiple locus/germlines. In the path <path>, takes 'homo-sapiens.germlines' to select locus and parameters
-g <path> multiple locus/germlines. In the path <path>, takes 'homo-sapiens.g' to select locus and parameters
Selecting '-g germline' processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations
Files different than 'homo-sapiens.germlines', for example for other species, can also be provided with -g <file>
Files different than 'homo-sapiens.g', for example for other species, can also be provided with -g <file>
Locus/recombinations
-d try to detect several D (experimental)
......@@ -245,14 +245,14 @@ Locus/recombinations
Using =-g germline/ -i= tests also some incomplete and unusual recombinations (locus with a =+= in their name),
and using =-g germline/ -i -2= further test unexpected recombinations (tagged as =xxx=).
See [[http://git.vidjil.org/blob/master/doc/locus.org][locus.org]] for information on the analyzable locus.
- Analyzed locus and parameters are configured through the =germline/homo-sapiens.germlines= file.
- Analyzed locus and parameters are configured through the =germline/homo-sapiens.g= file.
A =germline/isotypes.data= file is provided to look for sequences with, on one side, IGHJ (or even IGHV) genes,
and, on the other side, an IGH constant chain.
To select a custom set of TR or Ig locus, you may copy =germline/homo-sapiens.germlines= into a new file,
as for example =germline/custom.germlines=, and run Vidjil with =-g germline/custom.germlines -i -2=.
- Several =-g= options can be used, as for instance =-g germline -g germline/isotypes.germlines=.
To select a custom set of TR or Ig locus, you may copy =germline/homo-sapiens.g= into a new file,
as for example =germline/custom.g=, and run Vidjil with =-g germline/custom.g -i -2=.
- Several =-g= options can be used, as for instance =-g germline -g germline/isotypes.g=.
- One can use other germline sequences possibly by defining another
=.germlines= file that would refer to an alternative germline set or by
=.g= file that would refer to an alternative germline set or by
overwriting the existing germline sequences (in the FASTA file).
** Main algorithm parameters
......
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