Stop of quality issues but not on too many short reads

GoodstudyChina · Jul 17, 2019 · a446548 · a446548
1 parent 6e61f02
commit a446548
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/src/pipelines/canu/Defaults.pm b/src/pipelines/canu/Defaults.pm
@@ -907,7 +907,7 @@ sub setDefaults () {
 
     #####  Stopping conditions
 
-    setDefault("stopOnReadQuality", 0,     "Stop if a significant portion of the input data is too short or has quality value or base composition errors");
+    setDefault("stopOnReadQuality", 1,     "Stop if a significant portion of the input data has quality value or base composition errors");
     setDefault("stopOnLowCoverage", 10,    "Stop if raw, corrected or trimmed read coverage is low");
     setDefault("stopAfter",         undef, "Stop after a specific algorithm step is completed");
 

diff --git a/src/stores/sqStoreCreate.C b/src/stores/sqStoreCreate.C
@@ -727,8 +727,7 @@ createStore(const char *seqStoreName,
   if (nWARNS > 0.25 * (nLOADED))
     fprintf(stderr, "sqStoreCreate did NOT finish successfully; too many warnings.  Check your reads.\n");
 
-  if (nSKIPPED > 0.50 * (nLOADED))
-    fprintf(stderr, "sqStoreCreate did NOT finish successfully; too many short reads.  Check your reads!\n");
+  // do not output an error for too many short reads
 
   if ((bSKIPPED > 0.25 * (bSKIPPED + bLOADED)) ||
       (nWARNS   > 0.25 * (nSKIPPED + nLOADED)) ||