From 3b6edd753c52123d553151400443035f915637b9 Mon Sep 17 00:00:00 2001
From: Derek <derekwbarnett@gmail.com>
Date: Fri, 3 Sep 2010 00:35:05 -0400
Subject: [PATCH] Added IsIndexLoaded() public method to BamReader. Allows
 client to make sure index data is available before attempting any random
 access ops

---
 src/api/BamReader.cpp | 15 +++++++++++----
 src/api/BamReader.h   |  4 +++-
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 10aaa5e..f32b4fb 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -137,6 +137,7 @@ BamReader::~BamReader(void) {
 
 // file operations
 void BamReader::Close(void) { d->Close(); }
+bool BamReader::IsIndexLoaded(void) const { return d->IsIndexLoaded; }
 bool BamReader::IsOpen(void) const { return d->mBGZF.IsOpen; }
 bool BamReader::Jump(int refID, int position) { 
     d->Region.LeftRefID = refID;
@@ -360,6 +361,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
 void BamReader::BamReaderPrivate::ClearIndex(void) {
     delete NewIndex;
     NewIndex = 0;
+    IsIndexLoaded = false;
 }
 
 // closes the BAM file
@@ -393,11 +395,15 @@ bool BamReader::BamReaderPrivate::CreateIndex(bool useDefaultIndex) {
     else
         NewIndex = new BamToolsIndex(&mBGZF, Parent, IsBigEndian);
     
+    // build new index
     bool ok = true;
     ok &= NewIndex->Build();
+    IsIndexLoaded = ok;
+    
+    // attempt to save index data to file
     ok &= NewIndex->Write(Filename); 
     
-    // return success/fail
+    // return success/fail of both building & writing index
     return ok;
 }
 
@@ -515,7 +521,7 @@ bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
 
     // -----------------------------------------------------------------------
     // check for existing index 
-    if ( NewIndex == 0 ) return false; 
+    if ( !IsIndexLoaded || NewIndex == 0 ) return false; 
     // see if reference has alignments
     if ( !NewIndex->HasAlignments(refID) ) return false; 
     // make sure position is valid
@@ -605,8 +611,9 @@ bool BamReader::BamReaderPrivate::LoadIndex(void) {
         return false;
     }
     
-    // return success of loading index data
-    return NewIndex->Load(IndexFilename);
+    // return success of loading index data from file
+    IsIndexLoaded = NewIndex->Load(IndexFilename);
+    return IsIndexLoaded;
 }
 
 // populates BamAlignment with alignment data under file pointer, returns success/fail
diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index c93987b..5d4c83a 100644
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 9 July 2010 (DB)
+// Last modified: 2 September 2010 (DB)
 // ---------------------------------------------------------------------------
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -38,6 +38,8 @@ class BamReader {
 
         // close BAM file
         void Close(void);
+        // returns whether index data is loaded (i.e. reader is able to Jump() or not)
+        bool IsIndexLoaded(void) const;
         // returns whether reader is open for reading or not
         bool IsOpen(void) const;
         // performs random-access jump to reference, position
-- 
2.39.2