static rc_t prepare_compress( const compress_context * ctx,
KDirectory *dir, const KFile **src, KFile **dst )
{
KFile *temp = NULL;
rc_t rc = KDirectoryOpenFileRead ( dir, src, ctx->src_file );
DISP_RC( rc, "KDirectoryOpenFileRead() failed" );
if ( rc != 0 ) return rc;
rc = KDirectoryCreateFile ( dir, &temp, false, 0664, kcmInit, ctx->dst_file );
DISP_RC( rc, "KDirectoryCreateFile() failed" );
if ( rc == 0 )
switch( ctx->method )
{
case KC_GZIP : rc = KFileMakeGzipForWrite ( dst, temp );
DISP_RC( rc, "KFileMakeGzipForWrite() failed" );
break;
case KC_BZIP : rc = KFileMakeBzip2ForWrite ( dst, temp );
DISP_RC( rc, "KFileMakeBzip2ForWrite() failed" );
break;
case KC_SZIP : /* rc = KFileMakeSzipForWrite ( dst, temp ); */
rc = RC( rcExe, rcFile, rcPacking, rcFormat, rcUnknown );
DISP_RC( rc, "KFileMakeSzipForWrite() failed" );
break;
}
KFileRelease ( temp );
return rc;
}
static rc_t make_read_file( cg_dump_opts * opts, struct sg_lookup * lookup, KDirectory * dir, lane * l )
{
rc_t rc;
if ( opts->comp == oc_null )
{
l->reads = NULL;
rc = 0;
}
else
{
const char * ext;
switch( opts->comp )
{
case oc_none : ext = none_ext; break;
case oc_gzip : ext = gzip_ext; break;
case oc_bzip : ext = bzip_ext; break;
case oc_null : ext = none_ext; break;
}
rc = KDirectoryCreateFile ( dir, &l->reads, true, 0664, kcmCreate,
"%s%.*s_%03d.tsv%s", opts->prefix, l->name->len, l->name->addr, l->chunk, ext );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot create reads-file for lane '$(lane)' / chunk '$(chunk)'",
"lane=%S,chunk=%d", l->name, l->chunk ) );
}
else if ( opts->wbuff_size > 0 )
{
KFile * buffered;
rc = KBufWriteFileMakeWrite ( &buffered, l->reads, opts->wbuff_size );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot create buffered reads-file for lane '$(lane)' / chunk '$(chunk)'",
"lane=%S,chunk=%d", l->name, l->chunk ) );
}
else
{
KFileRelease( l->reads );
l->reads = buffered;
}
}
if ( rc == 0 && opts->comp != oc_none )
{
KFile * compressed = l->reads;
if ( opts->comp == oc_bzip )
{
rc = KFileMakeBzip2ForWrite ( &compressed, l->reads );
}
else if ( opts->comp == oc_gzip )
{
rc = KFileMakeGzipForWrite ( &compressed, l->reads );
}
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot create bzip reads-file for lane '$(lane)' / chunk '$(chunk)'",
"lane=%S,chunk=%d", l->name, l->chunk ) );
}
else
{
KFileRelease( l->reads );
l->reads = compressed;
}
}
if ( rc == 0 && opts->use_queue )
{
KFile * qf;
rc = KQueueFileMakeWrite ( &qf, l->reads, opts->qbytes, opts->qblock, opts->qtimeout );
if ( rc != 0 )
{
(void)PLOGERR( klogErr, ( klogErr, rc, "cannot create background writer for lane '$(lane)' / chunk '$(chunk)'",
"lane=%S,chunk=%d", l->name, l->chunk ) );
}
else
{
KFileRelease( l->reads );
l->reads = qf;
}
}
}
if ( rc == 0 )
{
rc = write_header( opts, lookup, l );
}
return rc;
}
rc_t init_out_redir( out_redir * self, out_redir_mode_t mode, const char * filename, size_t bufsize )
{
rc_t rc;
KFile *output_file;
if ( filename != NULL )
{
KDirectory *dir;
rc = KDirectoryNativeDir( &dir );
if ( rc != 0 )
LOGERR( klogInt, rc, "KDirectoryNativeDir() failed" );
else
{
rc = KDirectoryCreateFile ( dir, &output_file, false, 0664, kcmInit, "%s", filename );
KDirectoryRelease( dir );
}
}
else
rc = KFileMakeStdOut ( &output_file );
if ( rc == 0 )
{
KFile *temp_file;
/* wrap the output-file in compression, if requested */
switch ( mode )
{
case orm_gzip : rc = KFileMakeGzipForWrite( &temp_file, output_file ); break;
case orm_bzip2 : rc = KFileMakeBzip2ForWrite( &temp_file, output_file ); break;
case orm_uncompressed : break;
}
if ( rc == 0 )
{
if ( mode != orm_uncompressed )
{
KFileRelease( output_file );
output_file = temp_file;
}
/* wrap the output/compressed-file in buffering, if requested */
if ( bufsize != 0 )
{
rc = KBufFileMakeWrite( &temp_file, output_file, false, bufsize );
if ( rc == 0 )
{
KFileRelease( output_file );
output_file = temp_file;
}
}
if ( rc == 0 )
{
self->kfile = output_file;
self->org_writer = KOutWriterGet();
self->org_data = KOutDataGet();
self->pos = 0;
rc = KOutHandlerSet( out_redir_callback, self );
if ( rc != 0 )
LOGERR( klogInt, rc, "KOutHandlerSet() failed" );
}
}
}
return rc;
}
