Commit ee7acbae authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/algo.org: update documentation on -r option

parent c08059e5
......@@ -105,11 +105,8 @@ different clones. Setting =-w= to lower values is not recommended.
The following options control how many clones are output and analyzed.
#+BEGIN_EXAMPLE
Limit to keep a window
-r <nb> minimal number of reads containing a window (default: 10)
Limits to report a clone
-R <nb> minimal number of reads supporting a clone (default: 10)
-r <nb> minimal number of reads supporting a clone (default: 10)
-% <ratio> minimal percentage of reads supporting a clone (default: 0)
Limits to segment a clone
......@@ -117,13 +114,11 @@ Limits to segment a clone
-A reports and segments all clones (-r 0 -R 1 -% 0 -z 0), to be used only on very small datasets
#+END_EXAMPLE
The =-r/-R/-%= options are strong thresholds: if a clone does not have
The =-r/-%= options are strong thresholds: if a clone does not have
the requested number of reads, the clone is discarded (except when
using =-l=, see below).
The =-r= option is applied before the additional clustering, the
=-R/-%= options after it.
The default =-r 10 -R 10= options are meant to only output clones that
have a significant read support. You can safely put =-r 1 -R 1= if you
The default =-r 10= option is meant to only output clones that
have a significant read support. You can safely put =-r 1= if you
want to detect all clones starting from the first read (especially for
MRD detection).
......@@ -136,7 +131,7 @@ If you want to analyze more clones, you should use =-z 50= or
than 100 clones is often not useful since they can't be visualized easily
in the browser, and takes large computation time.
Note that even if a clone is not in the top 20 (or 50, or 100) but
still passes the =-R=, =-%= options, it is still reported in the .data
still passes the =-r=, =-%= options, it is still reported in the .data
file. If the clone is at some MRD point in the top 20 (or 50, or 100),
it will be fully analyzed/segmented by this other point (and then
collected by the =fuse.py= script, and then, on the browser, correctly
......
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