Commit 51947d0b authored by Mathieu Giraud's avatar Mathieu Giraud

algo/vidjil.cpp: export a warning when the coverage is low

See #2916.
parent b39e2205
...@@ -122,6 +122,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ; ...@@ -122,6 +122,7 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
// warn // warn
#define WARN_MAX_CLONES 100 #define WARN_MAX_CLONES 100
#define WARN_PERCENT_SEGMENTED 40 #define WARN_PERCENT_SEGMENTED 40
#define WARN_COVERAGE 0.6
// display // display
#define WIDTH_NB_READS 7 #define WIDTH_NB_READS 7
...@@ -1367,6 +1368,9 @@ int main (int argc, char **argv) ...@@ -1367,6 +1368,9 @@ int main (int argc, char **argv)
{"stop", kseg->getSequence().sequence.length()}, {"stop", kseg->getSequence().sequence.length()},
{"seq", repComp.getQuality()} {"seq", repComp.getQuality()}
}; };
if (repComp.getCoverage() < WARN_COVERAGE)
json_clone["warn"] = "Low coverage" ;
if (label.length()) if (label.length())
json_clone["label"] = label ; json_clone["label"] = label ;
......
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