From: Derek <derekwbarnett@gmail.com>
Date: Tue, 17 Aug 2010 20:39:44 +0000 (-0400)
Subject: Modified the way BGZF sets up uncompressed output. Modified BamWriter to support... 
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=2d6d143e041a08c2083a6857898ca36753317dad;p=bamtools.git

Modified the way BGZF sets up uncompressed output. Modified BamWriter to support uncompressed option.
---

diff --git a/BGZF.cpp b/BGZF.cpp
index 600e075..92afb96 100644
--- a/BGZF.cpp
+++ b/BGZF.cpp
@@ -17,7 +17,7 @@ using namespace BamTools;
 using std::string;
 using std::min;
 
-BgzfData::BgzfData(bool writeUncompressed)
+BgzfData::BgzfData(void)
     : UncompressedBlockSize(DEFAULT_BLOCK_SIZE)
     , CompressedBlockSize(MAX_BLOCK_SIZE)
     , BlockLength(0)
@@ -25,7 +25,7 @@ BgzfData::BgzfData(bool writeUncompressed)
     , BlockAddress(0)
     , IsOpen(false)
     , IsWriteOnly(false)
-    , IsWriteUncompressed(writeUncompressed)
+    , IsWriteUncompressed(false)
     , Stream(NULL)
     , UncompressedBlock(NULL)
     , CompressedBlock(NULL)
@@ -62,6 +62,7 @@ void BgzfData::Close(void) {
     // flush and close
     fflush(Stream);
     fclose(Stream);
+    IsWriteUncompressed = false;
     IsOpen = false;
 }
 
@@ -221,7 +222,7 @@ int BgzfData::InflateBlock(const int& blockLength) {
 }
 
 // opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing)
-bool BgzfData::Open(const string& filename, const char* mode) {
+bool BgzfData::Open(const string& filename, const char* mode, bool isWriteUncompressed ) {
 
     // determine open mode
     if ( strcmp(mode, "rb") == 0 )
@@ -254,8 +255,9 @@ bool BgzfData::Open(const string& filename, const char* mode) {
         return false;
     }
     
-    // set flag, return success
+    // set flags, return success
     IsOpen = true;
+    IsWriteUncompressed = isWriteUncompressed;
     return true;
 }
 
diff --git a/BGZF.h b/BGZF.h
index c5cd60b..37bcff7 100644
--- a/BGZF.h
+++ b/BGZF.h
@@ -93,7 +93,7 @@ struct BgzfData {
 
     // constructor & destructor
     public:
-        BgzfData(bool writeUncompressed = false);
+        BgzfData(void);
         ~BgzfData(void);
 
     // main interface methods
@@ -101,7 +101,7 @@ struct BgzfData {
         // closes BGZF file
         void Close(void);
         // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing)
-        bool Open(const std::string& filename, const char* mode);
+        bool Open(const std::string& filename, const char* mode, bool isWriteUncompressed = false);
         // reads BGZF data into a byte buffer
         int Read(char* data, const unsigned int dataLength);
         // seek to position in BGZF file
diff --git a/BamWriter.cpp b/BamWriter.cpp
index 5052eaa..f83ff1c 100644
--- a/BamWriter.cpp
+++ b/BamWriter.cpp
@@ -35,7 +35,7 @@ struct BamWriter::BamWriterPrivate {
 
     // "public" interface
     void Close(void);
-    bool Open(const string& filename, const string& samHeader, const RefVector& referenceSequences);
+    bool Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed);
     void SaveAlignment(const BamAlignment& al);
 
     // internal methods
@@ -65,8 +65,8 @@ void BamWriter::Close(void) {
 }
 
 // opens the alignment archive
-bool BamWriter::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences) {
-    return d->Open(filename, samHeader, referenceSequences);
+bool BamWriter::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed) {
+    return d->Open(filename, samHeader, referenceSequences, isWriteUncompressed);
 }
 
 // saves the alignment to the alignment archive
@@ -202,10 +202,10 @@ void BamWriter::BamWriterPrivate::EncodeQuerySequence(const string& query, strin
 }
 
 // opens the alignment archive
-bool BamWriter::BamWriterPrivate::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences) {
+bool BamWriter::BamWriterPrivate::Open(const string& filename, const string& samHeader, const RefVector& referenceSequences, bool isWriteUncompressed) {
 
     // open the BGZF file for writing, return failure if error
-    if ( !mBGZF.Open(filename, "wb") )
+    if ( !mBGZF.Open(filename, "wb", isWriteUncompressed) )
         return false;
 
     // ================
diff --git a/BamWriter.h b/BamWriter.h
index e8e7a14..b0cb6ce 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -34,7 +34,10 @@ class BamWriter {
         // closes the alignment archive
         void Close(void);
         // opens the alignment archive
-        bool Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences);
+        bool Open(const std::string& filename, 
+                  const std::string& samHeader, 
+                  const BamTools::RefVector& referenceSequences, 
+                  bool writeUncompressed = false);
         // saves the alignment to the alignment archive
         void SaveAlignment(const BamTools::BamAlignment& al);