--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/gzstream/gzstream.C	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,165 @@
+// ============================================================================
+// gzstream, C++ iostream classes wrapping the zlib compression library.
+// Copyright (C) 2001  Deepak Bandyopadhyay, Lutz Kettner
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+// ============================================================================
+//
+// File          : gzstream.C
+// Revision      : $Revision: 1.7 $
+// Revision_date : $Date: 2003/01/08 14:41:27 $
+// Author(s)     : Deepak Bandyopadhyay, Lutz Kettner
+//
+// Standard streambuf implementation following Nicolai Josuttis, "The
+// Standard C++ Library".
+// ============================================================================
+
+#include <gzstream.h>
+#include <iostream>
+#include <string.h>  // for memcpy
+
+#ifdef GZSTREAM_NAMESPACE
+namespace GZSTREAM_NAMESPACE {
+#endif
+
+// ----------------------------------------------------------------------------
+// Internal classes to implement gzstream. See header file for user classes.
+// ----------------------------------------------------------------------------
+
+// --------------------------------------
+// class gzstreambuf:
+// --------------------------------------
+
+gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
+    if ( is_open())
+        return (gzstreambuf*)0;
+    mode = open_mode;
+    // no append nor read/write mode
+    if ((mode & std::ios::ate) || (mode & std::ios::app)
+        || ((mode & std::ios::in) && (mode & std::ios::out)))
+        return (gzstreambuf*)0;
+    char  fmode[10];
+    char* fmodeptr = fmode;
+    if ( mode & std::ios::in)
+        *fmodeptr++ = 'r';
+    else if ( mode & std::ios::out)
+        *fmodeptr++ = 'w';
+    *fmodeptr++ = 'b';
+    *fmodeptr = '\0';
+    file = gzopen( name, fmode);
+    if (file == 0)
+        return (gzstreambuf*)0;
+    opened = 1;
+    return this;
+}
+
+gzstreambuf * gzstreambuf::close() {
+    if ( is_open()) {
+        sync();
+        opened = 0;
+        if ( gzclose( file) == Z_OK)
+            return this;
+    }
+    return (gzstreambuf*)0;
+}
+
+int gzstreambuf::underflow() { // used for input buffer only
+    if ( gptr() && ( gptr() < egptr()))
+        return * reinterpret_cast<unsigned char *>( gptr());
+
+    if ( ! (mode & std::ios::in) || ! opened)
+        return EOF;
+    // Josuttis' implementation of inbuf
+    int n_putback = gptr() - eback();
+    if ( n_putback > 4)
+        n_putback = 4;
+    memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
+
+    int num = gzread( file, buffer+4, bufferSize-4);
+    if (num <= 0) // ERROR or EOF
+        return EOF;
+
+    // reset buffer pointers
+    setg( buffer + (4 - n_putback),   // beginning of putback area
+          buffer + 4,                 // read position
+          buffer + 4 + num);          // end of buffer
+
+    // return next character
+    return * reinterpret_cast<unsigned char *>( gptr());
+}
+
+int gzstreambuf::flush_buffer() {
+    // Separate the writing of the buffer from overflow() and
+    // sync() operation.
+    int w = pptr() - pbase();
+    if ( gzwrite( file, pbase(), w) != w)
+        return EOF;
+    pbump( -w);
+    return w;
+}
+
+int gzstreambuf::overflow( int c) { // used for output buffer only
+    if ( ! ( mode & std::ios::out) || ! opened)
+        return EOF;
+    if (c != EOF) {
+        *pptr() = c;
+        pbump(1);
+    }
+    if ( flush_buffer() == EOF)
+        return EOF;
+    return c;
+}
+
+int gzstreambuf::sync() {
+    // Changed to use flush_buffer() instead of overflow( EOF)
+    // which caused improper behavior with std::endl and flush(),
+    // bug reported by Vincent Ricard.
+    if ( pptr() && pptr() > pbase()) {
+        if ( flush_buffer() == EOF)
+            return -1;
+    }
+    return 0;
+}
+
+// --------------------------------------
+// class gzstreambase:
+// --------------------------------------
+
+gzstreambase::gzstreambase( const char* name, int mode) {
+    init( &buf);
+    open( name, mode);
+}
+
+gzstreambase::~gzstreambase() {
+    buf.close();
+}
+
+void gzstreambase::open( const char* name, int open_mode) {
+    if ( ! buf.open( name, open_mode))
+        clear( rdstate() | std::ios::badbit);
+}
+
+void gzstreambase::close() {
+    if ( buf.is_open())
+        if ( ! buf.close())
+            clear( rdstate() | std::ios::badbit);
+}
+
+#ifdef GZSTREAM_NAMESPACE
+} // namespace GZSTREAM_NAMESPACE
+#endif
+
+// ============================================================================
+// EOF //