From 2b99e4788a395d5cde8c7d857fa5c6532b6222dd Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@bc.edu>
Date: Tue, 28 Sep 2010 17:44:12 -0400
Subject: [PATCH] added reader.Open checks to a number of tools

---
 src/toolkit/bamtools_convert.cpp  | 10 ++++++++--
 src/toolkit/bamtools_count.cpp    |  5 ++++-
 src/toolkit/bamtools_coverage.cpp |  5 ++++-
 src/toolkit/bamtools_sort.cpp     |  7 +++++--
 4 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index 86a3f9e..730a061 100644
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -160,7 +160,10 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
     
     // open input files
     BamMultiReader reader;
-    reader.Open(m_settings->InputFiles);
+    if (!reader.Open(m_settings->InputFiles, false)) {
+        cerr << "Could not open input files" << endl;
+        return false;
+    }
     m_references = reader.GetReferenceData();
 
     // set region if specified
@@ -463,7 +466,10 @@ void ConvertTool::ConvertToolPrivate::PrintJson(const BamAlignment& a) {
                 case('H') : 
                     m_out << "\""; 
                     while (tagData[index]) {
-                        m_out << tagData[index];
+                        if (tagData[index] == '\"')
+                            m_out << "\\\""; // escape for json
+                        else
+                            m_out << tagData[index];
                         ++index;
                     }
                     m_out << "\""; 
diff --git a/src/toolkit/bamtools_count.cpp b/src/toolkit/bamtools_count.cpp
index 20ed3ae..9d6623b 100644
--- a/src/toolkit/bamtools_count.cpp
+++ b/src/toolkit/bamtools_count.cpp
@@ -80,7 +80,10 @@ int CountTool::Run(int argc, char* argv[]) {
     
     // open reader without index
     BamMultiReader reader;
-    reader.Open(m_settings->InputFiles, false, true);
+    if (!reader.Open(m_settings->InputFiles, false, true)) {
+        cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
+        return 1;
+    }
 
     // alignment counter
     BamAlignment al;
diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp
index 5924edb..d46ba20 100644
--- a/src/toolkit/bamtools_coverage.cpp
+++ b/src/toolkit/bamtools_coverage.cpp
@@ -123,7 +123,10 @@ bool CoverageTool::CoverageToolPrivate::Run(void) {
     
     //open our BAM reader
     BamReader reader;
-    reader.Open(m_settings->InputBamFilename);
+    if (!reader.Open(m_settings->InputBamFilename)) {
+        cerr << "Could not open " << m_settings->InputBamFilename << " for reading." << endl;
+        return false;
+    }
     m_references = reader.GetReferenceData();
     
     // set up our output 'visitor'
diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp
index 83584a6..a6b3bba 100644
--- a/src/toolkit/bamtools_sort.cpp
+++ b/src/toolkit/bamtools_sort.cpp
@@ -197,7 +197,10 @@ bool SortTool::SortToolPrivate::GenerateSortedRuns(void) {
     
     // open input BAM file
     BamReader inputReader;
-    inputReader.Open(m_settings->InputBamFilename);
+    if (!inputReader.Open(m_settings->InputBamFilename)) {
+        cerr << "Could not open " << m_settings->InputBamFilename << " for reading." << endl;
+        return false;
+    }
     
     // get basic data that will be shared by all temp/output files 
     m_headerText = inputReader.GetHeaderText();
@@ -322,4 +325,4 @@ bool SortTool::SortToolPrivate::WriteTempFile(const vector<BamAlignment>& buffer
     // close temp file & return success
     tempWriter.Close();
     return true;
-}
\ No newline at end of file
+}
-- 
2.39.2