Commit e8ad8103 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/algo.org: help on labeled windows and on '-FaW' combo

parent da7abd24
......@@ -240,12 +240,14 @@ The =-A= option disables all these thresholds. This option should be
used only for test and debug purposes, on very small datasets, and
produce large file and takes huge computation times.
** Force to follow some sequences
Vidjil allows to specify a list of windows that must be followed
** Labeled windows
Vidjil allows to indicate that specific windows that must be followed
(even if those windows are 'rare', below the =-r/-%= thresholds).
The parameter =-l= is made for providing such a list in a file giving
one window by line like in the following example:
Such windows can be provided either with =-W <window>=, or with =-l <file>=.
The file given by =-l= should have one window by line, as in the following example:
#+BEGIN_EXAMPLE
TGTGCGAGAGATGGACGGGATACGTAAAACGACATATGGTTCGGGGTTTGGTGCTTTTGA my-clone-1
......@@ -257,6 +259,10 @@ The first column of the file is the window to be followed
while the remaining columns consist of the window's label.
In Vidjil output, the labels are output alongside their windows.
With the =-F= option, /only/ the labeld windows are kept. This allows
to quickly filter a set of reads, looking for a known window,
with the =-FaW <window>= options:
All the reads with this windows will be extracted to =out/seq/clone.fa-1=.
** Further clustering (experimental)
......
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