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/*
* sam.h
*
* Created on: Sep 23, 2009
* Author: Ben Langmead
*/
#ifndef SAM_H_
#define SAM_H_
#include "refmap.h"
#include "annot.h"
#include "pat.h"
#include "random_source.h"
#include "btypes.h"
class ReferenceMap;
class AnnotationMap;
class PatternSourcePerThread;
enum {
SAM_FLAG_PAIRED = 1,
SAM_FLAG_MAPPED_PAIRED = 2,
SAM_FLAG_UNMAPPED = 4,
SAM_FLAG_MATE_UNMAPPED = 8,
SAM_FLAG_QUERY_STRAND = 16,
SAM_FLAG_MATE_STRAND = 32,
SAM_FLAG_FIRST_IN_PAIR = 64,
SAM_FLAG_SECOND_IN_PAIR = 128,
SAM_FLAG_NOT_PRIMARY = 256,
SAM_FLAG_FAILS_CHECKS = 512,
SAM_FLAG_DUPLICATE = 1024
};
/**
* Sink that prints lines in SAM format:
*/
class SAMHitSink : public HitSink {
public:
/**
* Construct a single-stream VerboseHitSink (default)
*/
SAMHitSink(OutFileBuf* out,
int offBase,
ReferenceMap *rmap,
AnnotationMap *amap,
bool fullRef,
bool noQnameTrunc,
int defaultMapq,
DECL_HIT_DUMPS2) :
HitSink(out, PASS_HIT_DUMPS2),
offBase_(offBase), defaultMapq_(defaultMapq),
rmap_(rmap), amap_(amap), fullRef_(fullRef),
noQnameTrunc_(noQnameTrunc) { }
/**
* Construct a multi-stream VerboseHitSink with one stream per
* reference string (see --refout)
*/
SAMHitSink(size_t numOuts,
int offBase,
ReferenceMap *rmap,
AnnotationMap *amap,
bool fullRef,
int defaultMapq,
DECL_HIT_DUMPS2) :
HitSink(numOuts, PASS_HIT_DUMPS2),
offBase_(offBase), defaultMapq_(defaultMapq),
rmap_(rmap), amap_(amap), fullRef_(fullRef) { }
/**
* Append a SAM alignment to the given output stream.
*/
static void append(ostream& ss,
const Hit& h,
int mapq,
int xms,
const vector<string>* refnames,
ReferenceMap *rmap,
AnnotationMap *amap,
bool fullRef,
bool noQnameTrunc,
int offBase);
/**
* Append a SAM alignment for an aligned read to the given output
* stream.
*/
static void appendAligned(ostream& ss,
const Hit& h,
int mapq,
int xms,
const vector<string>* refnames,
ReferenceMap *rmap,
AnnotationMap *amap,
bool fullRef,
bool noQnameTrunc,
int offBase);
/**
* Append a verbose, readable hit to the output stream
* corresponding to the hit.
*/
virtual void append(ostream& ss, const Hit& h) {
SAMHitSink::append(ss, h, defaultMapq_, 0, _refnames, rmap_, amap_, fullRef_, noQnameTrunc_, offBase_);
}
/**
* Append a verbose, readable hit to the output stream
* corresponding to the hit.
*/
virtual void append(ostream& ss, const Hit& h, int mapq, int xms) {
SAMHitSink::append(ss, h, mapq, xms, _refnames, rmap_, amap_, fullRef_, noQnameTrunc_, offBase_);
}
/**
* Write the SAM header lines.
*/
void appendHeaders(OutFileBuf& os,
size_t numRefs,
const vector<string>& refnames,
bool color,
bool nosq,
ReferenceMap *rmap,
const TIndexOffU* plen,
bool fullRef,
bool noQnameTrunc,
const char *cmdline,
const char *rgline);
protected:
/**
*
*/
void reportUnOrMax(
PatternSourcePerThread& p,
vector<Hit>* hs,
bool un);
/**
* Report a verbose, human-readable alignment to the appropriate
* output stream.
*/
virtual void reportHit(const Hit& h) {
reportSamHit(h, defaultMapq_, 0);
}
/**
* Report a SAM alignment with the given mapping quality and XM
* field.
*/
virtual void reportSamHit(
const Hit& h,
int mapq,
int xms);
/**
* Report a batch of SAM alignments (e.g. two mates that should be
* printed together) with the given mapping quality and XM field.
*/
virtual void reportSamHits(
vector<Hit>& hs,
size_t start,
size_t end,
int mapq,
int xms);
/**
* See sam.cpp
*/
virtual void reportMaxed(vector<Hit>& hs, PatternSourcePerThread& p);
/**
* See sam.cpp
*/
virtual void reportUnaligned(PatternSourcePerThread& p) {
reportUnOrMax(p, NULL, true);
}
private:
int offBase_; /// Add this to reference offsets before outputting.
/// (An easy way to make things 1-based instead of
/// 0-based)
int defaultMapq_; /// Default mapping quality to report when one is
/// not specified
ReferenceMap *rmap_; /// mapping to reference coordinate system.
AnnotationMap *amap_; ///
bool fullRef_; /// print full reference name, not just up to whitespace
bool noQnameTrunc_; /// true -> don't truncate QNAME at first whitespace
};
#endif /* SAM_H_ */
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