Golden Helix patches

src/api/BamAlignment.h

@@ -127,7 +127,7 @@ struct API_EXPORT BamAlignment {
 
     //! \internal
     // internal utility methods
-    private:
+    //private: Still useful
         bool FindTag(const std::string& tag,
                      char*& pTagData,
                      const unsigned int& tagDataLength,
@@ -150,6 +150,7 @@ struct API_EXPORT BamAlignment {
             uint32_t    QueryNameLength;
             uint32_t    QuerySequenceLength;
             bool        HasCoreOnly;
+            int64_t     FileOffset;
 
             // constructor
             BamAlignmentSupportData(void)
@@ -160,7 +161,9 @@ struct API_EXPORT BamAlignment {
                 , HasCoreOnly(false)
             { }
         };
+    public: //Sometimes useful publicly
         BamAlignmentSupportData SupportData;
+    private:
         friend class Internal::BamReaderPrivate;
         friend class Internal::BamWriterPrivate;
 

src/api/BamConstants.h

@@ -126,10 +126,10 @@ const char BAM_DNA_PAD   = '*';
 
 // zlib & BGZF constants
 const char GZIP_ID1   = 31;
-const char GZIP_ID2   = 139;
+const char GZIP_ID2   = 139u;
 const char CM_DEFLATE = 8;
 const char FLG_FEXTRA = 4;
-const char OS_UNKNOWN = 255;
+const char OS_UNKNOWN = 255u;
 const char BGZF_XLEN  = 6;
 const char BGZF_ID1   = 66;
 const char BGZF_ID2   = 67;

src/api/BamIndex.h

@@ -12,6 +12,7 @@
 
 #include "api/api_global.h"
 #include "api/BamAux.h"
+#include "api/BamAlignment.h"
 #include <string>
 
 namespace BamTools {
@@ -20,6 +21,8 @@ namespace Internal {
     class BamReaderPrivate;
 } // namespace Internal
 
+typedef bool (*CreateIndexProgressCallback)(const BamAlignment& alignment, void* cbData);
+
 /*! \class BamTools::BamIndex
     \brief Provides methods for generating & loading BAM index files.
 
@@ -49,7 +52,9 @@ class API_EXPORT BamIndex {
     // index interface
     public:
         // builds index from associated BAM file & writes out to index file
-        virtual bool Create(void) =0;
+        virtual bool Create(std::string* indexFileName=0,
+                            CreateIndexProgressCallback cb=0,
+                            void* cbData=0) =0; // creates index file from BAM file
 
         // returns a human-readable description of the last error encountered
         std::string GetErrorString(void) { return m_errorString; }

src/api/BamReader.cpp

@@ -57,8 +57,11 @@ bool BamReader::Close(void) {
     \return \c true if index created OK
     \sa LocateIndex(), OpenIndex()
 */
-bool BamReader::CreateIndex(const BamIndex::IndexType& type) {
-    return d->CreateIndex(type);
+bool BamReader::CreateIndex(const BamIndex::IndexType& type,
+                            std::string* indexFileName,
+                            CreateIndexProgressCallback cb,
+                            void* cbData) {
+  return d->CreateIndex(type, indexFileName, cb, cbData);
 }
 
 /*! \fn std::string BamReader::GetErrorString(void) const

src/api/BamReader.h

@@ -90,7 +90,10 @@ class API_EXPORT BamReader {
         // ----------------------
 
         // creates an index file for current BAM file, using the requested index type
-        bool CreateIndex(const BamIndex::IndexType& type = BamIndex::STANDARD);
+        bool CreateIndex(const BamIndex::IndexType& type = BamIndex::STANDARD,
+                         std::string* indexFileName=0,
+                         CreateIndexProgressCallback cb=0,
+                         void* cbData=0);
         // returns true if index data is available
         bool HasIndex(void) const;
         // looks in BAM file's directory for a matching index file

src/api/IBamIODevice.h

@@ -24,6 +24,9 @@
 
 namespace BamTools {
 
+class IBamIODevice;
+typedef IBamIODevice* (*CreateBamIODeviceCallback)(const std::string& source);
+
 class API_EXPORT IBamIODevice {
 
     // enums
@@ -56,6 +59,8 @@ class API_EXPORT IBamIODevice {
         virtual bool IsOpen(void) const;
         virtual OpenMode Mode(void) const;
 
+        static void RegisterCreatorCallback(CreateBamIODeviceCallback cb);
+
     // internal methods
     protected:
         IBamIODevice(void); // hidden ctor

src/api/internal/bam/BamRandomAccessController_p.cpp

@@ -146,8 +146,11 @@ void BamRandomAccessController::ClearRegion(void) {
 }
 
 bool BamRandomAccessController::CreateIndex(BamReaderPrivate* reader,
-                                            const BamIndex::IndexType& type)
-{
+                                            const BamIndex::IndexType& type,
+                                            std::string* indexFileName,
+                                            CreateIndexProgressCallback cb,
+                                            void* cbData) {
+
     // skip if reader is invalid
     assert(reader);
     if ( !reader->IsOpen() ) {
@@ -166,7 +169,7 @@ bool BamRandomAccessController::CreateIndex(BamReaderPrivate* reader,
     }
 
     // attempt to build index from current BamReader file
-    if ( !newIndex->Create() ) {
+    if ( !newIndex->Create(indexFileName, cb, cbData) ) {
         const string indexError = newIndex->GetErrorString();
         const string message = "could not create index: \n\t" + indexError;
         SetErrorString("BamRandomAccessController::CreateIndex", message);

src/api/internal/bam/BamRandomAccessController_p.h

@@ -49,7 +49,10 @@ class BamRandomAccessController {
 
         // index methods
         void ClearIndex(void);
-        bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
+        bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type,
+                         std::string* indexFileName,
+                         CreateIndexProgressCallback cb,
+                         void* cbData);
         bool HasIndex(void) const;
         bool IndexHasAlignmentsForReference(const int& refId);
         bool LocateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& preferredType);

src/api/internal/bam/BamReader_p.cpp

@@ -70,16 +70,18 @@ bool BamReaderPrivate::Close(void) {
 }
 
 // creates an index file of requested type on current BAM file
-bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type) {
-
+bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type,
+                                   std::string* indexFileName,
+                                   CreateIndexProgressCallback cb,
+                                   void* cbData) {
     // skip if BAM file not open
     if ( !IsOpen() ) {
         SetErrorString("BamReader::CreateIndex", "cannot create index on unopened BAM file");
         return false;
     }
 
     // attempt to create index
-    if ( m_randomAccessController.CreateIndex(this, type) )
+    if ( m_randomAccessController.CreateIndex(this, type, indexFileName, cb, cbData) )
         return true;
     else {
         const string bracError = m_randomAccessController.GetErrorString();
@@ -230,10 +232,13 @@ void BamReaderPrivate::LoadHeaderData(void) {
 // populates BamAlignment with alignment data under file pointer, returns success/fail
 bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) {
 
+    alignment.SupportData.FileOffset = m_stream.Tell(); //Get the offset before we progress the stream
+
     // read in the 'block length' value, make sure it's not zero
     char buffer[sizeof(uint32_t)];
     fill_n(buffer, sizeof(uint32_t), 0);
-    m_stream.Read(buffer, sizeof(uint32_t));
+    if(m_stream.Read(buffer, sizeof(uint32_t)) < sizeof(uint32_t))
+      return false;
     alignment.SupportData.BlockLength = BamTools::UnpackUnsignedInt(buffer);
     if ( m_isBigEndian ) BamTools::SwapEndian_32(alignment.SupportData.BlockLength);
     if ( alignment.SupportData.BlockLength == 0 )

src/api/internal/bam/BamReader_p.h

@@ -62,7 +62,10 @@ class BamReaderPrivate {
         int GetReferenceID(const std::string& refName) const;
 
         // index operations
-        bool CreateIndex(const BamIndex::IndexType& type);
+        bool CreateIndex(const BamIndex::IndexType& type,
+                         std::string* indexFileName,
+                         CreateIndexProgressCallback cb,
+                         void* cbData);
         bool HasIndex(void) const;
         bool LocateIndex(const BamIndex::IndexType& preferredType);
         bool OpenIndex(const std::string& indexFilename);

src/api/internal/index/BamStandardIndex_p.cpp

@@ -262,7 +262,9 @@ void BamStandardIndex::CloseFile(void) {
 }
 
 // builds index from associated BAM file & writes out to index file
-bool BamStandardIndex::Create(void) {
+bool BamStandardIndex::Create(std::string* indexFileNamePreferred,
+                              CreateIndexProgressCallback progressCB,
+                              void* progressCBData) {
 
     // skip if BamReader is invalid or not open
     if ( m_reader == 0 || !m_reader->IsOpen() ) {
@@ -281,7 +283,11 @@ bool BamStandardIndex::Create(void) {
     try {
 
         // open new index file (read & write)
-        string indexFilename = m_reader->Filename() + Extension();
+        string indexFilename;
+        if(indexFileNamePreferred != 0)
+          indexFilename = *indexFileNamePreferred;
+        else
+          indexFilename = m_reader->Filename() + Extension();
         OpenFile(indexFilename, IBamIODevice::ReadWrite);
 
         // initialize BaiFileSummary with number of references
@@ -306,6 +312,17 @@ bool BamStandardIndex::Create(void) {
         BaiReferenceEntry refEntry;
         while ( m_reader->LoadNextAlignment(al) ) {
 
+            if(progressCB){
+              //Call progress CB for every read
+              if(!progressCB(al, progressCBData)){
+                //progressCB can return false indicating user canceled the index operation
+                CloseFile();
+                remove(indexFilename.c_str());
+                m_reader->Rewind();
+                return false;
+              }
+            }
+
             // changed to new reference
             if ( lastRefID != al.RefID ) {
 

src/api/internal/index/BamStandardIndex_p.h

@@ -113,7 +113,9 @@ class BamStandardIndex : public BamIndex {
     // BamIndex implementation
     public:
         // builds index from associated BAM file & writes out to index file
-        bool Create(void);
+        bool Create(std::string* indexFileName=0,
+                    CreateIndexProgressCallback cb=0,
+                    void* cbData=0);
         // returns whether reference has alignments or no
         bool HasAlignments(const int& referenceID) const;
         // attempts to use index data to jump to @region, returns success/fail

src/api/internal/index/BamToolsIndex_p.cpp

@@ -131,7 +131,9 @@ void BamToolsIndex::CloseFile(void) {
 }
 
 // builds index from associated BAM file & writes out to index file
-bool BamToolsIndex::Create(void) {
+bool BamToolsIndex::Create(std::string* indexFileNamePreferred,
+                           CreateIndexProgressCallback progressCB,
+                           void* progressCBData) {
 
     // skip if BamReader is invalid or not open
     if ( m_reader == 0 || !m_reader->IsOpen() ) {
@@ -149,7 +151,11 @@ bool BamToolsIndex::Create(void) {
 
     try {
         // open new index file (read & write)
-        const string indexFilename = m_reader->Filename() + Extension();
+        string indexFilename;
+        if(indexFileNamePreferred != 0)
+          indexFilename = *indexFileNamePreferred;
+        else
+          indexFilename = m_reader->Filename() + Extension();
         OpenFile(indexFilename, IBamIODevice::ReadWrite);
 
         // initialize BtiFileSummary with number of references
@@ -172,6 +178,17 @@ bool BamToolsIndex::Create(void) {
         BtiReferenceEntry refEntry;
         while ( m_reader->LoadNextAlignment(al) ) {
 
+            if(progressCB){
+              //Call progress CB every read
+              if(!progressCB(al, progressCBData)){
+                //progressCB can return false indicating user canceled the index operation
+                CloseFile();
+                remove(indexFilename.c_str());
+                m_reader->Rewind();
+                return false;
+              }
+            }
+
             // if moved to new reference
             if ( al.RefID != blockRefId ) {
 

src/api/internal/index/BamToolsIndex_p.h

@@ -108,7 +108,9 @@ class BamToolsIndex : public BamIndex {
     // BamIndex implementation
     public:
         // builds index from associated BAM file & writes out to index file
-        bool Create(void);
+        bool Create(std::string* indexFileName=0,
+                    CreateIndexProgressCallback cb=0,
+                    void* cbData=0);
         // returns whether reference has alignments or no
         bool HasAlignments(const int& referenceID) const;
         // attempts to use index data to jump to @region, returns success/fail

src/api/internal/io/BamDeviceFactory_p.cpp

@@ -9,29 +9,37 @@
 
 #include "api/internal/io/BamDeviceFactory_p.h"
 #include "api/internal/io/BamFile_p.h"
-#include "api/internal/io/BamFtp_p.h"
-#include "api/internal/io/BamHttp_p.h"
 #include "api/internal/io/BamPipe_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
 #include <iostream>
+#include <vector>
 using namespace std;
 
+static std::vector<CreateBamIODeviceCallback> m_callBacks;
+
 IBamIODevice* BamDeviceFactory::CreateDevice(const string& source) {
 
+    for(int i=0; i<m_callBacks.size(); i++){
+        IBamIODevice* device = m_callBacks[i](source);
+        if(device) //Callback did something with this source URL
+            return device;
+    }
+
     // check for requested pipe
     if ( source == "-" || source == "stdin" || source == "stdout" )
         return new BamPipe;
 
-    // check for HTTP prefix
-    if ( source.find("http://") == 0 )
-        return new BamHttp(source);
-
-    // check for FTP prefix
-    if ( source.find("ftp://") == 0 )
-        return new BamFtp(source);
-
     // otherwise assume a "normal" file
     return new BamFile(source);
 }
+
+void BamDeviceFactory::RegisterCreatorCallback(CreateBamIODeviceCallback cb)
+{
+    m_callBacks.push_back(cb);
+}
+
+void IBamIODevice::RegisterCreatorCallback(CreateBamIODeviceCallback cb){
+  BamDeviceFactory::RegisterCreatorCallback(cb);
+}

src/api/internal/io/BamDeviceFactory_p.h

@@ -29,6 +29,8 @@ namespace Internal {
 class BamDeviceFactory {
     public:
         static IBamIODevice* CreateDevice(const std::string& source);
+        static void RegisterCreatorCallback(CreateBamIODeviceCallback cb);
+
 };
 
 } // namespace Internal

src/api/internal/io/BamFtp_p.cpp

@@ -19,6 +19,21 @@ using namespace BamTools::Internal;
 #include <vector>
 using namespace std;
 
+static BamTools::IBamIODevice* createBamFtpDeviceCb(const std::string& source)
+{
+  if ( source.find("ftp://") == 0 )
+    return new BamFtp(source);
+  return 0;
+}
+
+struct RegisterBamFtpCallback{
+  RegisterBamFtpCallback(){
+    BamTools::IBamIODevice::RegisterCreatorCallback(createBamFtpDeviceCb);
+  }
+};
+static RegisterBamFtpCallback _cbInitializer; //Global ctor sets up BamFtp as device
+
+
 namespace BamTools {
 namespace Internal {