blast_dust.h

/*

   blast_dust.h		Adaptation of dust filtering in BLAST

*/

/* $Id: blast_dust.h,v 1.14 2005/11/16 14:31:36 madden Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
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 *  warranties of performance, merchantability or fitness for any particular
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 * ===========================================================================
 * 
 * Author: Ilya Dondoshansky
 *
 */

/** @file blast_dust.h
 * DUST filtering functions. (shouldn't this be merged with blast_filter?)
 * @todo FIXME: include reference?
 */

#ifndef __BLAST_DUST__
#define __BLAST_DUST__

/********************* Structure definitions ********************************/



#define TRUE 1
#define FALSE 0

/** Bit mask for obtaining a single base from a byte in ncbi2na format */
#define NCBI2NA_MASK 0x03


#ifdef __cplusplus
extern "C" {
#endif

/** Perform DUST low complexity filtering for a sequence buffer.
 * @param sequence Buffer for which to find low complexity locations [in]
 * @param length Length of the buffer [in]
 * @param offset At what offset in the buffer to start looking? [in]
 * @param level Level to be used in DUST algorithm [in]
 * @param window Window size for DUST [in]
 * @param linker Distance at which to link segments  [in]
 * @param dust_loc The locations found by dust [out]
 */
int blast_dust (unsigned char* __restrict sequence, const int length, int level, int window, int linker);

#ifdef __cplusplus
}
#endif
#endif /* !__BLAST_FILTER__ */