--- a/BEDTools-Version-2.14.3/src/utils/gzstream/gzstream.C	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,165 +0,0 @@
-// ============================================================================
-// 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 //