X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamReader_p.cpp;h=384e2fe59d50b5912b6bb2091a413813dd6339ae;hb=c1fc1c5423ca73a1b5bcbe790650821d73e5959c;hp=65b19f330a60c7fe9ac00cc1b992a98ce7b186d6;hpb=72f5b82ad353b4cc9d6f8153f1ad19cc387b9597;p=bamtools.git

diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index 65b19f3..384e2fe 100644
--- a/src/api/internal/BamReader_p.cpp
+++ b/src/api/internal/BamReader_p.cpp
@@ -9,6 +9,8 @@
 
 #include <api/BamConstants.h>
 #include <api/BamReader.h>
+#include <api/IBamIODevice.h>
+#include <api/internal/BamDeviceFactory_p.h>
 #include <api/internal/BamHeader_p.h>
 #include <api/internal/BamRandomAccessController_p.h>
 #include <api/internal/BamReader_p.h>
@@ -96,6 +98,9 @@ bool BamReaderPrivate::GetNextAlignment(BamAlignment& alignment) {
 // useful for operations requiring ONLY positional or other alignment-related information
 bool BamReaderPrivate::GetNextAlignmentCore(BamAlignment& alignment) {
 
+    if ( !m_stream.IsOpen() )
+        return false;
+
     // skip if region is set but has no alignments
     if ( m_randomAccessController.HasRegion() &&
          !m_randomAccessController.RegionHasAlignments() )
@@ -164,7 +169,7 @@ bool BamReaderPrivate::HasIndex(void) const {
 }
 
 bool BamReaderPrivate::IsOpen(void) const {
-    return m_stream.IsOpen;
+    return m_stream.IsOpen();
 }
 
 // load BAM header data
@@ -189,7 +194,7 @@ bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) {
 
     // swap core endian-ness if necessary
     if ( m_isBigEndian ) {
-        for ( int i = 0; i < Constants::BAM_CORE_SIZE; i+=sizeof(uint32_t) )
+        for ( unsigned int i = 0; i < Constants::BAM_CORE_SIZE; i+=sizeof(uint32_t) )
             BamTools::SwapEndian_32p(&x[i]);
     }
 
@@ -219,7 +224,7 @@ bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) {
     const unsigned int dataLength = alignment.SupportData.BlockLength - Constants::BAM_CORE_SIZE;
     char* allCharData = (char*)calloc(sizeof(char), dataLength);
 
-    if ( m_stream.Read(allCharData, dataLength) == (signed int)dataLength ) {
+    if ( m_stream.Read(allCharData, dataLength) == dataLength ) {
 
         // store 'allCharData' in supportData structure
         alignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength);
@@ -300,12 +305,11 @@ bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) {
 // opens BAM file (and index)
 bool BamReaderPrivate::Open(const string& filename) {
 
-    // close current BAM file if open
-    if ( m_stream.IsOpen )
-        Close();
+    // make sure we're starting with a fresh slate
+    Close();
 
     // attempt to open BgzfStream for reading
-    if ( !m_stream.Open(filename, "rb") ) {
+    if ( !m_stream.Open(filename, IBamIODevice::ReadOnly) ) {
         cerr << "BamReader ERROR: Could not open BGZF stream for " << filename << endl;
         return false;
     }
@@ -339,14 +343,23 @@ bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
 // returns BAM file pointer to beginning of alignment data
 bool BamReaderPrivate::Rewind(void) {
 
+    if ( !m_stream.IsOpen() ) {
+        cerr << "BRP::Rewind() - stream not open" << endl;
+        return false;
+    }
+
     // attempt rewind to first alignment
-    if ( !m_stream.Seek(m_alignmentsBeginOffset) )
+    if ( !m_stream.Seek(m_alignmentsBeginOffset) ) {
+        cerr << "BRP::Rewind() - could not seek to ABO (1st time)" << endl;
         return false;
+    }
 
     // verify that we can read first alignment
     BamAlignment al;
-    if ( !LoadNextAlignment(al) )
+    if ( !LoadNextAlignment(al) ) {
+        cerr << "BRP::Rewind() - could not read first alignment" << endl;
         return false;
+    }
 
     // reset region
     m_randomAccessController.ClearRegion();