Commit a75946f9 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp, doc/vidjil-algo.md: output files, 'segmented' -> 'analyzed'

parent cfdb171d
......@@ -98,8 +98,8 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define CLONES_FILENAME ".vdj.fa"
#define CLONE_FILENAME "clone.fa-"
#define WINDOWS_FILENAME ".windows.fa"
#define SEGMENTED_FILENAME ".segmented.vdj.fa"
#define UNSEGMENTED_FILENAME ".unsegmented.vdj.fa"
#define SEGMENTED_FILENAME ".analyzed.vdj.fa"
#define UNSEGMENTED_FILENAME ".not-analyzed.vdj.fa"
#define UNSEGMENTED_DETAIL_FILENAME ".fa"
#define AFFECTS_FILENAME ".affects"
#define EDGES_FILENAME ".edges"
......
......@@ -619,11 +619,11 @@ that can lead to few analyzed reads.
``` diff
Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)
-U, --out-analyzed output analyzed reads (in .segmented.vdj.fa file)
-U, --out-analyzed output analyzed reads (in .analyzed.vdj.fa file)
-u, --out-unanalyzed
-u output unanalyzed reads, gathered by cause, except for very short and 'too few V/J' reads (in *.fa files)
-uu output unanalyzed reads, gathered by cause, all reads (in *.fa files) (use only for debug)
-uuu output unanalyzed reads, all reads, including a .unsegmented.vdj.fa file (use only for debug)
-uuu output unanalyzed reads, all reads, including a .not-analyzed.vdj.fa file (use only for debug)
--out-reads output all reads by clones (clone.fa-*), to be used only on small datasets
-K, --out-affects output detailed k-mer affectation for each read (in .affects file) (use only for debug, for example -KX 100)
```
......@@ -640,7 +640,7 @@ Similarly, options are available to get the non analyzed reads:
it may be interesting to further study RNA-Seq datasets.
- `-uu` gives the same set of files, including **all** not analyzed reads (including `UNSEG too short` and `UNSEG too few V/J`),
and `-uuu` further outputs all these reads in a file `out/basename.unsegmented.vdj.fa`.
and `-uuu` further outputs all these reads in a file `out/basename.not-analyzed.vdj.fa`.
Again, as these options may generate large files, they are generally not recommended.
However, they are very useful in some situations, especially to understand why some dataset gives poor segmentation result.
......
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