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vidjil
vidjil
Commits
850123fa
Commit
850123fa
authored
May 12, 2020
by
Mathieu Giraud
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core/windowExtractor.{h,cpp}, vidjil.cpp: W09 when interrupted during first pass
parent
2478e5c5
Pipeline
#143914
passed with stages
in 39 minutes and 33 seconds
Changes
3
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1
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3 changed files
with
10 additions
and
4 deletions
+10
-4
algo/core/windowExtractor.cpp
algo/core/windowExtractor.cpp
+5
-2
algo/core/windowExtractor.h
algo/core/windowExtractor.h
+4
-1
algo/vidjil.cpp
algo/vidjil.cpp
+1
-1
No files found.
algo/core/windowExtractor.cpp
View file @
850123fa
...
...
@@ -18,7 +18,8 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
map
<
string
,
string
>
&
windows_labels
,
bool
only_labeled_windows
,
bool
keep_unsegmented_as_clone
,
double
nb_expected
,
int
nb_reads_for_evalue
,
VirtualReadScore
*
scorer
)
{
VirtualReadScore
*
scorer
,
SampleOutput
*
output
)
{
init_stats
();
WindowsStorage
*
windowsStorage
=
new
WindowsStorage
(
windows_labels
);
...
...
@@ -34,7 +35,9 @@ WindowsStorage *WindowExtractor::extract(OnlineBioReader *reads,
if
(
global_interrupted
)
{
cout
<<
WARNING_STRING
<<
"Interrupted after processing "
<<
nb_reads
<<
" reads"
<<
endl
;
string
msg
=
"Interrupted after processing "
+
string_of_int
(
nb_reads
)
+
" reads"
;
if
(
output
)
output
->
add_warning
(
"W09"
,
msg
,
LEVEL_WARN
);
cout
<<
WARNING_STRING
<<
msg
<<
endl
;
break
;
}
...
...
algo/core/windowExtractor.h
View file @
850123fa
...
...
@@ -12,6 +12,7 @@
#include "read_storage.h"
#include "bioreader.hpp"
#include "read_score.h"
#include "output.h"
#define NB_BINS_CLONES 10
#define MAX_VALUE_BINS_CLONES 1000
...
...
@@ -53,6 +54,7 @@ class WindowExtractor {
* @param nb_expected: maximal e-value of the segmentation
* @param nb_reads_for_evalue: number of reads, used for e-value computation. Can be approximate or faked.
* @param scorer: how reads are scored (only the best ones are keeped for large clones)
* @param output: global output, used here for warnings
* @return a pointer to a WindowsStorage that will contain all the windows.
* It is a pointer so that the WindowsStorage is not duplicated.
* @post Statistics on segmentation will be provided through the getSegmentationStats() methods
...
...
@@ -63,7 +65,8 @@ class WindowExtractor {
map
<
string
,
string
>
&
windows_labels
,
bool
only_labeled_windows
=
false
,
bool
keep_unsegmented_as_clone
=
false
,
double
nb_expected
=
THRESHOLD_NB_EXPECTED
,
int
nb_reads_for_evalue
=
1
,
VirtualReadScore
*
scorer
=
&
DEFAULT_READ_SCORE
);
VirtualReadScore
*
scorer
=
&
DEFAULT_READ_SCORE
,
SampleOutput
*
output
=
NULL
);
/**
* @return the average length of sequences whose segmentation has been classified as seg
...
...
algo/vidjil.cpp
View file @
850123fa
...
...
@@ -1133,7 +1133,7 @@ int main (int argc, char **argv)
windows_labels
,
only_labeled_windows
,
keep_unsegmented_as_clone
,
expected_value_kmer
,
nb_reads_for_evalue
,
readScorer
);
readScorer
,
&
output
);
windowsStorage
->
setIdToAll
();
size_t
nb_total_reads
=
we
.
getNbReads
();
...
...
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