Issue #988: proceed reading from GTF after a warning that exon end is…

… past chromosome end.
alexdobin · Aug 15, 2020 · 1fe083b · 1fe083b
1 parent 10930be
commit 1fe083b
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,4 @@
+* Issue #988: proceed reading from GTF after a warning that exon end is past chromosome end.
 * Issue #978: fixed corrupted transcriptInfo.tab in genome generation for cases where GTF file contains extra chromosomes not present in FASTA files.
 * Issue #945: otuput GX/GN for --soloFeatures GeneFull .
 

diff --git a/source/ErrorWarning.cpp b/source/ErrorWarning.cpp
@@ -5,10 +5,12 @@
 #include "TimeFunctions.h"
 #include "GlobalVariables.h"
 
-void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, Parameters &P) {
+void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2, int errorInt, Parameters &P)
+{
+    if (P.runThreadN>1) 
+        pthread_mutex_lock(&g_threadChunks.mutexError);
     time_t timeCurrent;
     time( &timeCurrent);
-    if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexError);
     if (streamOut1.good()) {
         streamOut1 << "\n" << messageOut << endl << timeMonthDayTime(timeCurrent) <<" ...... FATAL ERROR, exiting\n"  <<flush;
     };
@@ -20,14 +22,16 @@ void exitWithError(string messageOut, ostream &streamOut1, ostream &streamOut2,
     exit(errorInt);
 };
 
-void warningMessage(string messageOut, ostream &streamOut1, ostream &streamOut2, Parameters &P) {
-    time_t timeCurrent;
-    time( &timeCurrent);
-    if (P.runThreadN>1) pthread_mutex_lock(&g_threadChunks.mutexError);
+void warningMessage(string messageOut, ostream &streamOut1, ostream &streamOut2, Parameters &P)
+{
+    if (P.runThreadN>1) 
+        pthread_mutex_lock(&g_threadChunks.mutexError);
     if (streamOut1.good()) {
         streamOut1 << "!!!!! WARNING: " << messageOut <<endl;
     };
     if (streamOut2.good()) {
         streamOut2 << "!!!!! WARNING: " << messageOut <<endl;
     };
+    if (P.runThreadN>1) 
+        pthread_mutex_unlock(&g_threadChunks.mutexError);    
 };