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vidjil
vidjil
Commits
fa86f7de
Commit
fa86f7de
authored
Mar 25, 2014
by
Mathieu Giraud
Browse files
vidjil.cpp: warn if there are less than WARN_RATIO_SEGMENTED (0.4) reads
parent
89cc6c14
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
fa86f7de
...
...
@@ -110,6 +110,9 @@ enum { CMD_WINDOWS, CMD_ANALYSIS, CMD_SEGMENT } ;
#define DEFAULT_CLUSTER_COST Cluster
#define DEFAULT_SEGMENT_COST VDJ
// warn
#define WARN_RATIO_SEGMENTED 0.4
// display
#define WIDTH_NB_READS 7
#define WIDTH_NB_CLONES 3
...
...
@@ -633,12 +636,20 @@ int main (int argc, char **argv)
// nb_segmented is the main denominator for the following (but will be normalized)
int
nb_segmented
=
we
.
getNbSegmented
(
TOTAL_SEG_AND_WINDOW
);
float
ratio_segmented
=
100
*
(
float
)
nb_segmented
/
nb_total_reads
;
cout
<<
" ==> found "
<<
windowsStorage
->
size
()
<<
" "
<<
w
<<
"-windows"
<<
" in "
<<
nb_segmented
<<
" segments"
<<
" ("
<<
setprecision
(
3
)
<<
100
*
(
float
)
nb_segmented
/
nb_total_reads
<<
"%)"
<<
" ("
<<
setprecision
(
3
)
<<
ratio_segmented
<<
"%)"
<<
" inside "
<<
nb_total_reads
<<
" sequences"
<<
endl
;
// warn if there are too few segmented sequences
if
(
ratio_segmented
<
WARN_RATIO_SEGMENTED
)
{
cout
<<
" ! There are not so many CDR3 windows found in this set of reads."
<<
endl
;
cout
<<
" ! If this is unexpected, check the germline (-G) and try to change seed parameters (-k)."
<<
endl
;
}
cout
<<
" # av. length"
<<
endl
;
for
(
int
i
=
0
;
i
<
STATS_SIZE
;
i
++
)
...
...
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