Commit c54f9d21 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp, doc/algo.org: defaults to -z 100

With all locus analyzed, the -z 100 option gives a better description of the lympohcyte population.
Note that the FineSegmenter is more than two times faster than in the 2015.10 release.
parent 6be92245
......@@ -75,7 +75,7 @@
#define DEFAULT_READS "./data/Stanford_S22.fasta"
#define DEFAULT_MIN_READS_CLONE 5
#define DEFAULT_MAX_REPRESENTATIVES 100
#define DEFAULT_MAX_CLONES 20
#define DEFAULT_MAX_CLONES 100
#define DEFAULT_RATIO_READS_CLONE 0.0
#define NO_LIMIT "all"
......
......@@ -289,7 +289,7 @@ Limits to report a clone (or a window)
Limits to further analyze some clones
-y <nb> maximal number of clones computed with a representative ('all': no limit) (default: 100)
-z <nb> maximal number of clones to be analyzed with a full V(D)J designation ('all': no limit, do not use) (default: 20)
-z <nb> maximal number of clones to be analyzed with a full V(D)J designation ('all': no limit, do not use) (default: 100)
-A reports and segments all clones (-r 1 -% 0 -y all -z all), to be used only on very small datasets
#+END_EXAMPLE
......@@ -310,19 +310,19 @@ The =-z= option limits the number of clones that are fully analyzed,
/with their V(D)J segmentation/, in particular to enable the web application
to display the clones on the grid (otherwise they are displayed on the
'?/?' axis).
If you want to analyze more clones, you should use =-z 50= or
=-z 100=. It is not recommended to use larger values: outputting more
than 100 clones is often not useful since they can not be visualized easily
If you want to analyze more clones, you should use =-z 200= or
=-z 500=. It is not recommended to use larger values: outputting more
than 500 clones is often not useful since they can not be visualized easily
in the web application, and takes large computation time (full dynamic programming,
see below).
Note that even if a clone is not in the top 20 (or 50, or 100) but
Note that even if a clone is not in the top 100 (or 200, or 500) but
still passes the =-r=, =-%= options, it is still reported in both the =.vidjil=
and =.vdj.fa= files. If the clone is at some MRD point in the top 20 (or 50, or 100),
and =.vdj.fa= files. If the clone is at some MRD point in the top 100 (or 200, or 500),
it will be fully analyzed/segmented by this other point (and then
collected by the =fuse.py= script, using representatives computed at this
other point, and then, on the web application, correctly displayed on the grid).
*Thus is advised to leave the default* =-y 100 -z 20= *options
*Thus is advised to leave the default* =-z 100= *option
for the majority of uses.*
The =-A= option disables all these thresholds. This option should be
......
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