235 lines
8.2 KiB
C
235 lines
8.2 KiB
C
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/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef ALIGNER_SEED_POLICY_H_
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#define ALIGNER_SEED_POLICY_H_
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#include "scoring.h"
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#include "simple_func.h"
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#define DEFAULT_SEEDMMS 0
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#define DEFAULT_SEEDLEN 22
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#define DEFAULT_IVAL SIMPLE_FUNC_SQRT
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#define DEFAULT_IVAL_A 1.15f
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#define DEFAULT_IVAL_B 0.0f
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#define DEFAULT_UNGAPPED_HITS 6
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/**
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* Encapsulates the set of all parameters that affect what the
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* SeedAligner does with reads.
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*/
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class SeedAlignmentPolicy {
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public:
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/**
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* Parse alignment policy when provided in this format:
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* <lab>=<val>;<lab>=<val>;<lab>=<val>...
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*
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* And label=value possibilities are:
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*
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* Bonus for a match
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* -----------------
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*
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* MA=xx (default: MA=0, or MA=2 if --local is set)
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*
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* xx = Each position where equal read and reference characters match up
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* in the alignment contriubtes this amount to the total score.
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*
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* Penalty for a mismatch
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* ----------------------
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*
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* MMP={Cxx|Q|RQ} (default: MMP=C6)
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*
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* Cxx = Each mismatch costs xx. If MMP=Cxx is specified, quality
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* values are ignored when assessing penalities for mismatches.
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* Q = Each mismatch incurs a penalty equal to the mismatched base's
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* value.
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* R = Each mismatch incurs a penalty equal to the mismatched base's
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* rounded quality value. Qualities are rounded off to the
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* nearest 10, and qualities greater than 30 are rounded to 30.
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*
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* Penalty for position with N (in either read or reference)
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* ---------------------------------------------------------
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*
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* NP={Cxx|Q|RQ} (default: NP=C1)
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*
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* Cxx = Each alignment position with an N in either the read or the
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* reference costs xx. If NP=Cxx is specified, quality values are
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* ignored when assessing penalities for Ns.
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* Q = Each alignment position with an N in either the read or the
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* reference incurs a penalty equal to the read base's quality
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* value.
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* R = Each alignment position with an N in either the read or the
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* reference incurs a penalty equal to the read base's rounded
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* quality value. Qualities are rounded off to the nearest 10,
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* and qualities greater than 30 are rounded to 30.
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*
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* Penalty for a read gap
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* ----------------------
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*
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* RDG=xx,yy (default: RDG=5,3)
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*
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* xx = Read gap open penalty.
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* yy = Read gap extension penalty.
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*
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* Total cost incurred by a read gap = xx + (yy * gap length)
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*
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* Penalty for a reference gap
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* ---------------------------
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*
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* RFG=xx,yy (default: RFG=5,3)
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*
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* xx = Reference gap open penalty.
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* yy = Reference gap extension penalty.
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*
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* Total cost incurred by a reference gap = xx + (yy * gap length)
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*
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* Minimum score for valid alignment
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* ---------------------------------
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*
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* MIN=xx,yy (defaults: MIN=-0.6,-0.6, or MIN=0.0,0.66 if --local is set)
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*
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* xx,yy = For a read of length N, the total score must be at least
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* xx + (read length * yy) for the alignment to be valid. The
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* total score is the sum of all negative penalties (from
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* mismatches and gaps) and all positive bonuses. The minimum
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* can be negative (and is by default in global alignment mode).
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*
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* N ceiling
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* ---------
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*
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* NCEIL=xx,yy (default: NCEIL=0.0,0.15)
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*
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* xx,yy = For a read of length N, the number of alignment
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* positions with an N in either the read or the
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* reference cannot exceed
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* ceiling = xx + (read length * yy). If the ceiling is
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* exceeded, the alignment is considered invalid.
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*
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* Seeds
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* -----
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*
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* SEED=mm,len,ival (default: SEED=0,22)
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*
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* mm = Maximum number of mismatches allowed within a seed.
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* Must be >= 0 and <= 2. Note that 2-mismatch mode is
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* not fully sensitive; i.e. some 2-mismatch seed
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* alignments may be missed.
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* len = Length of seed.
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* ival = Interval between seeds. If not specified, seed
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* interval is determined by IVAL.
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*
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* Seed interval
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* -------------
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*
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* IVAL={L|S|C},xx,yy (default: IVAL=S,1.0,0.0)
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*
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* L = let interval between seeds be a linear function of the
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* read length. xx and yy are the constant and linear
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* coefficients respectively. In other words, the interval
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* equals a * len + b, where len is the read length.
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* Intervals less than 1 are rounded up to 1.
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* S = let interval between seeds be a function of the sqaure
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* root of the read length. xx and yy are the
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* coefficients. In other words, the interval equals
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* a * sqrt(len) + b, where len is the read length.
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* Intervals less than 1 are rounded up to 1.
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* C = Like S but uses cube root of length instead of square
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* root.
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*
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* Example 1:
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*
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* SEED=1,10,5 and read sequence is TGCTATCGTACGATCGTAC:
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*
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* The following seeds are extracted from the forward
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* representation of the read and aligned to the reference
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* allowing up to 1 mismatch:
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*
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* Read: TGCTATCGTACGATCGTACA
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*
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* Seed 1+: TGCTATCGTA
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* Seed 2+: TCGTACGATC
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* Seed 3+: CGATCGTACA
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*
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* ...and the following are extracted from the reverse-complement
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* representation of the read and align to the reference allowing
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* up to 1 mismatch:
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*
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* Seed 1-: TACGATAGCA
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* Seed 2-: GATCGTACGA
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* Seed 3-: TGTACGATCG
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*
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* Example 2:
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*
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* SEED=1,20,20 and read sequence is TGCTATCGTACGATC. The seed
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* length is 20 but the read is only 15 characters long. In this
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* case, Bowtie2 automatically shrinks the seed length to be equal
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* to the read length.
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*
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* Read: TGCTATCGTACGATC
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*
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* Seed 1+: TGCTATCGTACGATC
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* Seed 1-: GATCGTACGATAGCA
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*
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* Example 3:
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*
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* SEED=1,10,10 and read sequence is TGCTATCGTACGATC. Only one seed
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* fits on the read; a second seed would overhang the end of the read
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* by 5 positions. In this case, Bowtie2 extracts one seed.
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*
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* Read: TGCTATCGTACGATC
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*
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* Seed 1+: TGCTATCGTA
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* Seed 1-: TACGATAGCA
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*/
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static void parseString(
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const std::string& s,
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bool local,
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bool noisyHpolymer,
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bool ignoreQuals,
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int& bonusMatchType,
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int& bonusMatch,
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int& penMmcType,
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int& penMmcMax,
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int& penMmcMin,
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int& penScMax,
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int& penScMin,
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int& penNType,
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int& penN,
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int& penRdExConst,
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int& penRfExConst,
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int& penRdExLinear,
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int& penRfExLinear,
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SimpleFunc& costMin,
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SimpleFunc& nCeil,
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bool& nCatPair,
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int& multiseedMms,
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int& multiseedLen,
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SimpleFunc& multiseedIval,
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size_t& failStreak,
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size_t& seedRounds,
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SimpleFunc* penCanIntronLen = NULL,
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SimpleFunc* penNoncanIntronLen = NULL);
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};
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#endif /*ndef ALIGNER_SEED_POLICY_H_*/
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