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sam.h
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sam.h
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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef SAM_H_
#define SAM_H_
#include <string>
#include "ds.h"
#include "read.h"
#include "util.h"
#include "aligner_result.h"
#include "scoring.h"
enum {
// Comments use language from v1.4-r962 spec
SAM_FLAG_PAIRED = 1, // templ. having mult. frag.s in sequencing
SAM_FLAG_MAPPED_PAIRED = 2, // each frag properly aligned
SAM_FLAG_UNMAPPED = 4, // fragment unmapped
SAM_FLAG_MATE_UNMAPPED = 8, // next fragment in template unmapped
SAM_FLAG_QUERY_STRAND = 16, // SEQ is reverse comp'ed from original
SAM_FLAG_MATE_STRAND = 32, // next fragment SEQ reverse comp'ed
SAM_FLAG_FIRST_IN_PAIR = 64, // first fragment in template
SAM_FLAG_SECOND_IN_PAIR = 128, // last fragment in template
SAM_FLAG_NOT_PRIMARY = 256, // secondary alignment
SAM_FLAG_FAILS_CHECKS = 512, // not passing quality controls
SAM_FLAG_DUPLICATE = 1024 // PCR or optical duplicate
};
class AlnRes;
class AlnFlags;
class AlnSetSumm;
/**
* Encapsulates all the various ways that a user may wish to customize SAM
* output.
*/
class SamConfig {
typedef EList<std::string> StrList;
typedef EList<size_t> LenList;
public:
SamConfig(
const StrList& refnames, // reference sequence names
const LenList& reflens, // reference sequence lengths
bool truncQname, // truncate read name to 255?
bool omitsec, // omit secondary SEQ/QUAL
bool noUnal, // omit unaligned reads
const std::string& pg_id, // id
const std::string& pg_pn, // name
const std::string& pg_vn, // version
const std::string& pg_cl, // command-line
const std::string& rgs, // read groups string
bool print_as,
bool print_xs,
bool print_xss,
bool print_yn,
bool print_xn,
bool print_x0,
bool print_x1,
bool print_xm,
bool print_xo,
bool print_xg,
bool print_nm,
bool print_md,
bool print_yf,
bool print_yi,
bool print_ym,
bool print_yp,
bool print_yt,
bool print_ys,
bool print_zs,
bool print_xr,
bool print_xt,
bool print_xd,
bool print_xu,
bool print_ye, // streak of failed DPs at end
bool print_yl, // longest streak of failed DPs
bool print_yu, // index of last succeeded DP
bool print_xp, // print seed hit information
bool print_yr, // # redundant seed hits
bool print_zb, // # Ftab lookups
bool print_zr, // # redundant path checks
bool print_zf, // # FM Index ops
bool print_zm, // FM Index op string for best-first search
bool print_zi, // # seed extend loop iters
bool print_zp,
bool print_zu,
bool print_zt) :
truncQname_(truncQname),
omitsec_(omitsec),
noUnal_(noUnal),
pg_id_(pg_id),
pg_pn_(pg_pn),
pg_vn_(pg_vn),
pg_cl_(pg_cl),
rgs_(rgs),
refnames_(refnames),
reflens_(reflens),
print_as_(print_as), // alignment score of best alignment
print_xs_(print_xs), // alignment score of second-best alignment
print_xss_(print_xss),
print_yn_(print_yn), // minimum valid score and perfect score
print_xn_(print_xn),
print_x0_(print_x0),
print_x1_(print_x1),
print_xm_(print_xm),
print_xo_(print_xo),
print_xg_(print_xg),
print_nm_(print_nm),
print_md_(print_md),
print_yf_(print_yf),
print_yi_(print_yi),
print_ym_(print_ym),
print_yp_(print_yp),
print_yt_(print_yt),
print_ys_(print_ys),
print_zs_(print_zs),
print_xr_(print_xr),
print_xt_(print_xt), // time elapsed in microseconds
print_xd_(print_xd), // DP extend attempts
print_xu_(print_xu), // ungapped extend attempts
print_ye_(print_ye), // streak of failed DPs at end
print_yl_(print_yl), // longest streak of failed DPs
print_yu_(print_yu), // index of last succeeded DP
print_xp_(print_xp), // print seed hit information
print_yr_(print_yr), // index of last succeeded DP
print_zb_(print_zb), // # Ftab lookups
print_zr_(print_zr), // # redundant path checks
print_zf_(print_zf), // # FM Index ops
print_zm_(print_zm), // FM Index op string for best-first search
print_zi_(print_zi), // # seed extend loop iters
print_zp_(print_zp), // # seed extend loop iters
print_zu_(print_zu), // # seed extend loop iters
print_zt_(print_zt) // extra features for MAPQ estimation
{
assert_eq(refnames_.size(), reflens_.size());
}
/**
* Print a reference name in a way that doesn't violate SAM's character
* constraints. \*|[!-()+-<>-~][!-~]*
*/
void printRefName(
BTString& o,
const std::string& name)
const;
/**
* Print a :Z optional field where certain characters (whitespace, colon
* and percent) are escaped using % escapes.
*/
template<typename T>
void printOptFieldEscapedZ(BTString& o, const T& s) const {
size_t len = s.length();
for(size_t i = 0; i < len; i++) {
if(s[i] < 33 || s[i] > 126 || s[i] == ':' || s[i] == '%') {
// percent-encode it
o.append('%');
int ms = s[i] >> 4;
int ls = s[i] & 15;
assert_range(0, 15, ms);
assert_range(0, 15, ls);
o.append("0123456789ABCDEF"[ms]);
o.append("0123456789ABCDEF"[ls]);
} else {
o.append(s[i]);
}
}
}
/**
* Print a :Z optional field where newline characters are escaped using %
* escapes.
*/
template<typename T>
void printOptFieldNewlineEscapedZ(BTString& o, const T& s) const {
size_t len = s.length();
for(size_t i = 0; i < len; i++) {
if(s[i] == 10 || s[i] == 13 || s[i] == '%') {
// percent-encode it
o.append('%');
int ms = s[i] >> 4;
int ls = s[i] & 15;
assert_range(0, 15, ms);
assert_range(0, 15, ls);
o.append("0123456789ABCDEF"[ms]);
o.append("0123456789ABCDEF"[ls]);
} else {
o.append(s[i]);
}
}
}
/**
* Print a read name in a way that doesn't violate SAM's character
* constraints. [!-?A-~]{1,255} (i.e. [33, 63], [65, 126])
*/
template<typename TStr>
void printReadName(
BTString& o,
const TStr& name,
bool omitSlashMate)
const
{
size_t namelen = name.length();
if(omitSlashMate &&
namelen >= 2 &&
name[namelen-2] == '/' &&
(name[namelen-1] == '1' || name[namelen-1] == '2' || name[namelen-1] == '3'))
{
namelen -= 2;
}
if(truncQname_ && namelen > 255) {
namelen = 255;
}
for(size_t i = 0; i < namelen; i++) {
if(truncQname_ && isspace(name[i])) {
return;
}
o.append(name[i]);
}
}
/**
* Print a reference name given a reference index.
*/
void printRefNameFromIndex(
BTString& o,
size_t i)
const;
/**
* Print SAM header to given output buffer.
*/
void printHeader(
BTString& o,
const std::string& rgid,
const std::string& rgs,
bool printHd,
bool printSq,
bool printPg)
const;
/**
* Print the @HD header line to the given string.
*/
void printHdLine(BTString& o, const char *samver) const;
/**
* Print the @SQ header lines to the given string.
*/
void printSqLines(BTString& o) const;
/**
* Print the @PG header line to the given string.
*/
void printPgLine(BTString& o) const;
/**
* Print the optional flags to the given string.
*/
void printAlignedOptFlags(
BTString& o, // output buffer
bool first, // first opt flag printed is first overall?
const Read& rd, // the read
const Read* rdo, // the opposite read
AlnRes& res, // individual alignment result
StackedAln& staln, // stacked alignment
const AlnFlags& flags, // alignment flags
const AlnSetSumm& summ, // summary of alignments for this read
const SeedAlSumm& ssm, // seed alignment summary
const PerReadMetrics& prm, // per-read metics
const Scoring& sc, // scoring scheme
const char *mapqInp) // inputs to MAPQ calculation
const;
/**
* Print the optional flags to the given string.
*/
void printEmptyOptFlags(
BTString& o, // output buffer
bool first, // first opt flag printed is first overall?
const Read& rd, // the read
const AlnFlags& flags, // alignment flags
const AlnSetSumm& summ, // summary of alignments for this read
const SeedAlSumm& ssm, // seed alignment summary
const PerReadMetrics& prm, // per-read metrics
const Scoring& sc) // scoring scheme
const;
/**
* Print optional flags that that have been preserve from BAM input
*/
void printPreservedOptFlags(BTString& o, const Read& rd) const;
/**
* Return true iff we should try to obey the SAM spec's recommendations
* that:
*
* SEQ and QUAL of secondary alignments should be set to ‘*’ to reduce the
* file size.
*/
bool omitSecondarySeqQual() const {
return omitsec_;
}
bool omitUnalignedReads() const {
return noUnal_;
}
protected:
bool truncQname_; // truncate QNAME to 255 chars?
bool omitsec_; // omit secondary
bool noUnal_; // omit unaligned reads
std::string pg_id_; // @PG ID: Program record identifier
std::string pg_pn_; // @PG PN: Program name
std::string pg_vn_; // @PG VN: Program version
std::string pg_cl_; // @PG CL: Program command-line
std::string rgs_; // Read-group string to add to all records
const StrList& refnames_; // reference sequence names
const LenList& reflens_; // reference sequence lengths
// Which alignment flags to print?
// Following are printed by BWA-SW
bool print_as_; // AS:i: Alignment score generated by aligner
bool print_xs_; // XS:i: Suboptimal alignment score
bool print_xss_;// Xs:i: Best invalid alignment score found
bool print_yn_; // YN:i:, Yn:i: minimum valid score and perfect score
bool print_xn_; // XN:i: Number of ambiguous bases in the referenece
// Following are printed by BWA
bool print_x0_; // X0:i: Number of best hits
bool print_x1_; // X1:i: Number of sub-optimal best hits
bool print_xm_; // XM:i: Number of mismatches in the alignment
bool print_xo_; // XO:i: Number of gap opens
bool print_xg_; // XG:i: Number of gap extensions (incl. opens)
bool print_nm_; // NM:i: Edit dist. to the ref, Ns count, clipping doesn't
bool print_md_; // MD:Z: String for mms. [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)*2
// Following are Bowtie2-specific
bool print_yf_; // YF:i: Read was filtered out?
bool print_yi_; // YI:Z: Summary of inputs to MAPQ calculation
bool print_ym_; // YM:i: Read was repetitive when aligned unpaired?
bool print_yp_; // YP:i: Read was repetitive when aligned paired?
bool print_yt_; // YT:Z: String representing alignment type
bool print_ys_; // YS:i: Score of other mate
bool print_zs_; // ZS:i: Pseudo-random seed
bool print_xr_; // XR:Z: Original read string
bool print_xt_; // XT:i: Time taken to align
bool print_xd_; // XD:i: DP problems
bool print_xu_; // XU:i: ungapped alignment
bool print_ye_; // YE:i: streak of failed DPs at end
bool print_yl_; // YL:i: longest streak of failed DPs
bool print_yu_; // YU:i: index of last succeeded DP
bool print_xp_; // XP:BI: seed hit information
bool print_yr_; // YR:i: # redundant seed hits
bool print_zb_; // ZB:i: # Ftab lookups
bool print_zr_; // ZR:i: # redundant path checks
bool print_zf_; // ZF:i: # FM Index ops
bool print_zm_; // ZM:i: FM ops string for best-first search
bool print_zi_; // ZI:i: # extend loop iters
bool print_zp_; // ZP:i: Score of best/second-best paired-end alignment
bool print_zu_; // ZU:i: Score of best/second-best unpaired alignment
bool print_zt_; // ZT:Z: Extra features for MAPQ estimation
};
#endif /* SAM_H_ */