BGI/BASE/src/2bwt/blast_dust.h

   1 /*
   2
   3    blast_dust.h        Adaptation of dust filtering in BLAST
   4
   5 */
   6
   7 /* $Id: blast_dust.h,v 1.14 2005/11/16 14:31:36 madden Exp $
   8  * ===========================================================================
   9  *
  10  *                            PUBLIC DOMAIN NOTICE
  11  *               National Center for Biotechnology Information
  12  *
  13  *  This software/database is a "United States Government Work" under the
  14  *  terms of the United States Copyright Act.  It was written as part of
  15  *  the author's official duties as a United States Government employee and
  16  *  thus cannot be copyrighted.  This software/database is freely available
  17  *  to the public for use. The National Library of Medicine and the U.S.
  18  *  Government have not placed any restriction on its use or reproduction.
  19  *
  20  *  Although all reasonable efforts have been taken to ensure the accuracy
  21  *  and reliability of the software and data, the NLM and the U.S.
  22  *  Government do not and cannot warrant the performance or results that
  23  *  may be obtained by using this software or data. The NLM and the U.S.
  24  *  Government disclaim all warranties, express or implied, including
  25  *  warranties of performance, merchantability or fitness for any particular
  26  *  purpose.
  27  *
  28  *  Please cite the author in any work or product based on this material.
  29  *
  30  * ===========================================================================
  31  *
  32  * Author: Ilya Dondoshansky
  33  *
  34  */
  35
  36 /** @file blast_dust.h
  37  * DUST filtering functions. (shouldn't this be merged with blast_filter?)
  38  * @todo FIXME: include reference?
  39  */
  40
  41 #ifndef __BLAST_DUST__
  42 #define __BLAST_DUST__
  43
  44 /********************* Structure definitions ********************************/
  45
  46
  47
  48 #define TRUE 1
  49 #define FALSE 0
  50
  51 /** Bit mask for obtaining a single base from a byte in ncbi2na format */
  52 #define NCBI2NA_MASK 0x03
  53
  54
  55 #ifdef __cplusplus
  56 extern "C" {
  57 #endif
  58
  59 /** Perform DUST low complexity filtering for a sequence buffer.
  60  * @param sequence Buffer for which to find low complexity locations [in]
  61  * @param length Length of the buffer [in]
  62  * @param offset At what offset in the buffer to start looking? [in]
  63  * @param level Level to be used in DUST algorithm [in]
  64  * @param window Window size for DUST [in]
  65  * @param linker Distance at which to link segments  [in]
  66  * @param dust_loc The locations found by dust [out]
  67  */
  68 int blast_dust (unsigned char* __restrict sequence, const int length, int level, int window, int linker);
  69
  70 #ifdef __cplusplus
  71 }
  72 #endif
  73 #endif /* !__BLAST_FILTER__ */