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/* $Id: hspfilter_besthit.h,v 1.2 2009/06/01 16:04:31 kazimird Exp $
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* ===========================================================================
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* National Center for Biotechnology Information
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* This software/database is a "United States Government Work" under the
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* terms of the United States Copyright Act. It was written as part of
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* the author's official duties as a United States Government employee and
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* thus cannot be copyrighted. This software/database is freely available
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* to the public for use. The National Library of Medicine and the U.S.
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* Government have not placed any restriction on its use or reproduction.
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* Although all reasonable efforts have been taken to ensure the accuracy
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* and reliability of the software and data, the NLM and the U.S.
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* Government do not and cannot warrant the performance or results that
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* may be obtained by using this software or data. The NLM and the U.S.
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* Government disclaim all warranties, express or implied, including
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* warranties of performance, merchantability or fitness for any particular
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* Please cite the author in any work or product based on this material.
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* ===========================================================================
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/** @file hspfilter_besthit.h
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* Implementation of a number of BlastHSPWriters to save hits from
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* a BLAST search, and subsequently return them in sorted order.
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#ifndef ALGO_BLAST_CORE__HSPFILTER_BESTHIT__H
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#define ALGO_BLAST_CORE__HSPFILTER_BESTHIT__H
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#include <algo/blast/core/ncbi_std.h>
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#include <algo/blast/core/blast_program.h>
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#include <algo/blast/core/blast_options.h>
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#include <algo/blast/core/blast_hspfilter.h>
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#include <algo/blast/core/blast_hits.h>
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#include <connect/ncbi_core.h>
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/************************************************************************/
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/** The "best hit" writer
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Prune the hsp_list for each query and keeps only the best ones.
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1. For a pair of hits A and B, check based on 10% overhangs whether
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A can be dropped because of B due to end points of A being within
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10% extension of B and vice versa. Note that this would allow A
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to be dropped even if it is at most 20% longer than B.
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2. If A can be dropped because of B, check if Evalue(A) >= Evalue(B);
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that is A has the same or worse evalue than B. Do the same check for
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whether B can be dropped because of A.
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3. If A can still be dropped because of B, check if density(A) <= density(B).
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Do the same check for whether B can be dropped because of A.
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4. If only one can be dropped, then drop that one. If both are mutually
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replaceable, use length criteria and drop the shorter one
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only if it is at least 10% shorter (90% coverage).
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So, essentially length coverage is being used a tie-breaker and if the
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tie-breaker does not break the tie, both alignments are kept. Above is not
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very different than what you have now, just rearranged in conditions
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so that we do not have non-deterministic behavior between a pair of
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alignments. We could still have issues with cascades where A was dropped
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because of B and then B gets dropped because of C, but A would not have
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been dropped because of C becuase of condition 4. However, I think this
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will be extremely rare.
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/// Default value for overhang
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#define kBestHit_OverhangDflt 0.1
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/// Minimum value for overhang
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#define kBestHit_OverhangMin 0.0
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/// Maximum value for overhang
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#define kBestHit_OverhangMax 0.5
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/// Default value for score_edge
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#define kBestHit_ScoreEdgeDflt 0.1
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/// Minimum value for score_edge
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#define kBestHit_ScoreEdgeMin 0.0
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/// Maximum value for score_edge
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#define kBestHit_ScoreEdgeMax 0.5
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/** Keeps parameters used in best hit algorithm.*/
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typedef struct BlastHSPBestHitParams {
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EBlastProgramType program;/**< program type. */
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Int4 prelim_hitlist_size; /**< number of hits saved during preliminary
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double overhang; /**< overhang used in condition 1. */
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double score_edge; /**< fraction of score margin in condition 4*/
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} BlastHSPBestHitParams;
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/** create a set of parameters
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* @param program Blast program type.[in]
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* @param hit_options field hitlist_size and hsp_num_max needed, a pointer to
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* this structure will be stored on resulting structure.[in]
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* @param overhang Specifies the ratio of overhang to length, which is used to
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determine if hit A is contained in hit B
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* @return the pointer to the allocated parameter
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BlastHSPBestHitParams*
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BlastHSPBestHitParamsNew(const BlastHitSavingOptions* hit_options,
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const BlastHSPBestHitOptions* best_hit_opts);
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/** Deallocates the BlastHSPBestHitParams structure passed in
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* @param opts structure to deallocate [in]
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BlastHSPBestHitParams*
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BlastHSPBestHitParamsFree(BlastHSPBestHitParams* opts);
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/** WriterInfo and PipeInfo to create a best hit writer/pipe
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* @param params Specifies writer parameters. [in]
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* @return the newly allocated writer/pipe info
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BlastHSPBestHitInfoNew(BlastHSPBestHitParams* params);
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BlastHSPBestHitPipeInfoNew(BlastHSPBestHitParams* params);
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#endif /* !ALGO_BLAST_CORE__HSPFILTER_BESTHIT__H */
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algo/blast/core/hspfilter_besthit.h
