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vidjil
vidjil
Commits
c752bd3c
Commit
c752bd3c
authored
Mar 17, 2015
by
Mathieu Giraud
Browse files
vidjil.cpp: MAX12, '-2' without '-1'
n+1 indexes: the n regular ones, and the common one for MAX12.
parent
b14ff728
Changes
1
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Inline
Side-by-side
algo/vidjil.cpp
View file @
c752bd3c
...
...
@@ -162,7 +162,7 @@ void usage(char *progname, bool advanced)
cerr
<<
"Experimental options (do not use)"
<<
endl
<<
" -I ignore k-mers common to different germline systems (experimental, must be used with -g, do not use)"
<<
endl
<<
" -1 use a unique index for all germline systems (experimental, must be used with -g, do not use)"
<<
endl
<<
" -2 try to detect unexpected recombinations (experimental, must be used with -g
1
, do not use)"
<<
endl
<<
" -2 try to detect unexpected recombinations (experimental, must be used with -g, do not use)"
<<
endl
<<
" -! keep unsegmented reads as clones, taking for junction the complete sequence, to be used on very small datasets (for example -!AX 20)"
<<
endl
<<
endl
...
...
@@ -789,12 +789,16 @@ int main (int argc, char **argv)
if
(
!
multi_germline_one_index_per_germline
)
{
multigermline
->
build_with_one_index
(
seed
,
true
);
}
if
(
multi_germline_unexpected_recombinations
)
{
if
(
!
multigermline
->
index
)
{
multigermline
->
build_with_one_index
(
seed
,
false
);
}
Germline
*
pseudo
=
new
Germline
(
PSEUDO_GERMLINE_MAX12
,
'x'
,
-
10
,
80
);
pseudo
->
index
=
multigermline
->
index
;
multigermline
->
germlines
.
push_back
(
pseudo
);
}
}
if
(
multi_germline_mark
)
...
...
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