Added informative error messages to fasta.cpp and FaQCs.cpp to help …

…users diagnose corrupted input files.
LANL-Bioinformatics · Aug 17, 2018 · 54c31da · 54c31da
1 parent 0fa3653
commit 54c31da
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Showing 4 changed files with 17 additions and 4 deletions.
diff --git a/ChangeLog.txt b/ChangeLog.txt
@@ -38,4 +38,7 @@ Version 2.07b (Mar 16, 2018)
 	  vector += function).
 
 Version 2.08 (May 1, 2018)
-	* Fixed a bug in ployA option which required argument should turn off. ( options.cpp)
+	* Fixed a bug due to the "--polyA" command line argument expecting an argument (it should be a boolean flag).
+
+Version 2.09 (Aug 17, 2018)
+	* Added informative error messages to fasta.cpp and FaQCs.cpp to help users diagnose corrupted input files.
diff --git a/FaQCs.cpp b/FaQCs.cpp
@@ -370,10 +370,10 @@ void process_paired(vector<size_t> &m_filter_stats,
 		if(ret1 != ret2){
 
 			if(ret1){
-				cerr << "Found an unmatched read one" << endl;
+				cerr << "Did not find a match to read one: " << r1.def << endl;
 			}
 			else{
-				cerr << "Found an unmatched read two" << endl;
+				cerr << "Did not find a match to read two: " << r2.def << endl;
 			}
 
 			throw __FILE__ "I/O error";

diff --git a/README.md b/README.md
@@ -60,7 +60,7 @@ FULL USAGE
 
 ```     
 Usage: FaQCs [options] [-u unpaired.fastq] -p reads1.fastq reads2.fastq -d out_directory
-Version 2.08
+Version 2.09
 Input File(s):
 	-u			<File> Unpaired reads
 	-1			<File> First paired read file

diff --git a/fastq.cpp b/fastq.cpp
@@ -60,6 +60,8 @@ bool next_read(gzFile m_fin, string &m_def, string &m_seq, string &m_quality)
 	while(true){
 
 		if(gzgets(m_fin, buffer, buffer_len) == NULL){
+
+			cerr << "Error in read: " << m_def << endl;
 			throw __FILE__ ":next_read: Unable to read sequence";
 		}
 
@@ -77,10 +79,14 @@ bool next_read(gzFile m_fin, string &m_def, string &m_seq, string &m_quality)
 	// Skip the '+'. Note that we *don't* actually test to make sure we read a single '+' on a line
 	// by itself.
 	if(gzgets(m_fin, buffer, buffer_len) == NULL){
+
+		cerr << "Error in read: " << m_def << endl;
 		throw __FILE__ ":next_read: Unable to read '+'";
 	}
 
 	if( strpbrk(buffer, "\n\r") == NULL ){
+
+		cerr << "Error in read: " << m_def << endl;
 		throw __FILE__ ":next_read: Error reading '+' delimiter";
 	}
 
@@ -93,6 +99,8 @@ bool next_read(gzFile m_fin, string &m_def, string &m_seq, string &m_quality)
 	while(true){
 
 		if(gzgets(m_fin, buffer, buffer_len) == NULL){
+
+			cerr << "Error in read: " << m_def << endl;
 			throw __FILE__ ":next_read: Unable to read quality";
 		}
 
@@ -108,6 +116,8 @@ bool next_read(gzFile m_fin, string &m_def, string &m_seq, string &m_quality)
 	}
 
 	if( m_seq.size() != m_quality.size() ){
+
+		cerr << "Error in read: " << m_def << endl;
 		throw __FILE__ ":next_read: |Sequence| != |Quality|";
 	}