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2025-01-18 13:09:52 +00:00
/*
* 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 PAT_H_
#define PAT_H_
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <vector>
#include <string>
#include <cstring>
#include <ctype.h>
#include <fstream>
#include "alphabet.h"
#include "assert_helpers.h"
#include "tokenize.h"
#include "random_source.h"
#include "threading.h"
#include "filebuf.h"
#include "qual.h"
#include "search_globals.h"
#include "sstring.h"
#include "ds.h"
#include "read.h"
#include "util.h"
extern bool threeN;
/**
* Classes and routines for reading reads from various input sources.
*/
using namespace std;
/**
* Calculate a per-read random seed based on a combination of
* the read data (incl. sequence, name, quals) and the global
* seed in '_randSeed'.
*/
static inline uint32_t genRandSeed(const BTDnaString& qry,
const BTString& qual,
const BTString& name,
uint32_t seed)
{
// Calculate a per-read random seed based on a combination of
// the read data (incl. sequence, name, quals) and the global
// seed
uint32_t rseed = (seed + 101) * 59 * 61 * 67 * 71 * 73 * 79 * 83;
size_t qlen = qry.length();
// Throw all the characters of the read into the random seed
for(size_t i = 0; i < qlen; i++) {
int p = (int)qry[i];
assert_leq(p, 4);
size_t off = ((i & 15) << 1);
rseed ^= (p << off);
}
// Throw all the quality values for the read into the random
// seed
for(size_t i = 0; i < qlen; i++) {
int p = (int)qual[i];
assert_leq(p, 255);
size_t off = ((i & 3) << 3);
rseed ^= (p << off);
}
// Throw all the characters in the read name into the random
// seed
size_t namelen = name.length();
for(size_t i = 0; i < namelen; i++) {
int p = (int)name[i];
if(p == '/') break;
assert_leq(p, 255);
size_t off = ((i & 3) << 3);
rseed ^= (p << off);
}
return rseed;
}
/**
* Parameters affecting how reads and read in.
*/
struct PatternParams {
PatternParams(
int format_,
bool fileParallel_,
uint32_t seed_,
bool useSpinlock_,
bool solexa64_,
bool phred64_,
bool intQuals_,
bool fuzzy_,
int sampleLen_,
int sampleFreq_,
uint32_t skip_) :
format(format_),
fileParallel(fileParallel_),
seed(seed_),
useSpinlock(useSpinlock_),
solexa64(solexa64_),
phred64(phred64_),
intQuals(intQuals_),
fuzzy(fuzzy_),
sampleLen(sampleLen_),
sampleFreq(sampleFreq_),
skip(skip_) { }
int format; // file format
bool fileParallel; // true -> wrap files with separate PairedPatternSources
uint32_t seed; // pseudo-random seed
bool useSpinlock; // use spin locks instead of pthreads
bool solexa64; // true -> qualities are on solexa64 scale
bool phred64; // true -> qualities are on phred64 scale
bool intQuals; // true -> qualities are space-separated numbers
bool fuzzy; // true -> try to parse fuzzy fastq
int sampleLen; // length of sampled reads for FastaContinuous...
int sampleFreq; // frequency of sampled reads for FastaContinuous...
uint32_t skip; // skip the first 'skip' patterns
};
/**
* Encapsulates a synchronized source of patterns; usually a file.
* Optionally reverses reads and quality strings before returning them,
* though that is usually more efficiently done by the concrete
* subclass. Concrete subclasses should delimit critical sections with
* calls to lock() and unlock().
*/
class PatternSource {
public:
PatternSource(const PatternParams& p) :
seed_(p.seed),
readCnt_(0),
numWrappers_(0),
doLocking_(true),
useSpinlock_(p.useSpinlock),
mutex()
{
}
virtual ~PatternSource() { }
/**
* Call this whenever this PatternSource is wrapped by a new
* WrappedPatternSourcePerThread. This helps us keep track of
* whether locks will be contended.
*/
void addWrapper() {
lock();
numWrappers_++;
unlock();
}
/**
* The main member function for dispensing patterns.
*
* Returns true iff a pair was parsed succesfully.
*/
virtual bool nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName);
/**
* The main member function for dispensing patterns.
*/
virtual bool nextRead(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/**
* Implementation to be provided by concrete subclasses. An
* implementation for this member is only relevant for formats that
* can read in a pair of reads in a single transaction with a
* single input source. If paired-end input is given as a pair of
* parallel files, this member should throw an error and exit.
*/
virtual bool nextReadPairImpl(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired) = 0;
/**
* Implementation to be provided by concrete subclasses. An
* implementation for this member is only relevant for formats
* where individual input sources look like single-end-read
* sources, e.g., formats where paired-end reads are specified in
* parallel read files.
*/
virtual bool nextReadImpl(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done) = 0;
/// Reset state to start over again with the first read
virtual void reset() { readCnt_ = 0; }
/**
* Concrete subclasses call lock() to enter a critical region.
* What constitutes a critical region depends on the subclass.
*/
void lock() {
if(!doLocking_) return; // no contention
mutex.lock();
}
/**
* Concrete subclasses call unlock() to exit a critical region
* What constitutes a critical region depends on the subclass.
*/
void unlock() {
if(!doLocking_) return; // no contention
mutex.unlock();
}
/**
* Return a new dynamically allocated PatternSource for the given
* format, using the given list of strings as the filenames to read
* from or as the sequences themselves (i.e. if -c was used).
*/
static PatternSource* patsrcFromStrings(
const PatternParams& p,
const EList<string>& qs,
size_t nthreads = 1);
/**
* Return the number of reads attempted.
*/
TReadId readCnt() const { return readCnt_ - 1; }
int paired_type; // 1 - left or unpaird, 2-right
// int align_times = 0;
protected:
uint32_t seed_;
/// The number of reads read by this PatternSource
TReadId readCnt_;
int numWrappers_; /// # threads that own a wrapper for this PatternSource
bool doLocking_; /// override whether to lock (true = don't override)
/// User can ask to use the normal pthreads-style lock even if
/// spinlocks is enabled and compiled in. This is sometimes better
/// if we expect bad I/O latency on some reads.
bool useSpinlock_;
MUTEX_T mutex;
};
/**
* Abstract parent class for synhconized sources of paired-end reads
* (and possibly also single-end reads).
*/
class PairedPatternSource {
public:
PairedPatternSource(const PatternParams& p) : mutex_m(), seed_(p.seed) {}
virtual ~PairedPatternSource() { }
virtual void addWrapper() = 0;
virtual void reset() = 0;
virtual bool nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName) = 0;
virtual pair<TReadId, TReadId> readCnt() const = 0;
/**
* Lock this PairedPatternSource, usually because one of its shared
* fields is being updated.
*/
void lock() {
mutex_m.lock();
}
/**
* Unlock this PairedPatternSource.
*/
void unlock() {
mutex_m.unlock();
}
/**
* Given the values for all of the various arguments used to specify
* the read and quality input, create a list of pattern sources to
* dispense them.
*/
static PairedPatternSource* setupPatternSources(
const EList<string>& si, // singles, from argv
const EList<string>& m1, // mate1's, from -1 arg
const EList<string>& m2, // mate2's, from -2 arg
const EList<string>& m12, // both mates on each line, from --12 arg
#ifdef USE_SRA
const EList<string>& sra_accs,
#endif
const EList<string>& q, // qualities associated with singles
const EList<string>& q1, // qualities associated with m1
const EList<string>& q2, // qualities associated with m2
const PatternParams& p, // read-in params
size_t nthreads,
bool verbose); // be talkative?
protected:
MUTEX_T mutex_m; /// mutex for syncing over critical regions
uint32_t seed_;
};
/**
* Encapsulates a synchronized source of both paired-end reads and
* unpaired reads, where the paired-end must come from parallel files.
*/
class PairedSoloPatternSource : public PairedPatternSource {
public:
PairedSoloPatternSource(
const EList<PatternSource*>* src,
const PatternParams& p) :
PairedPatternSource(p),
cur_(0),
src_(src)
{
assert(src_ != NULL);
for(size_t i = 0; i < src_->size(); i++) {
assert((*src_)[i] != NULL);
}
}
virtual ~PairedSoloPatternSource() { delete src_; }
/**
* Call this whenever this PairedPatternSource is wrapped by a new
* WrappedPatternSourcePerThread. This helps us keep track of
* whether locks within PatternSources will be contended.
*/
virtual void addWrapper() {
for(size_t i = 0; i < src_->size(); i++) {
(*src_)[i]->addWrapper();
}
}
/**
* Reset this object and all the PatternSources under it so that
* the next call to nextReadPair gets the very first read pair.
*/
virtual void reset() {
for(size_t i = 0; i < src_->size(); i++) {
(*src_)[i]->reset();
}
cur_ = 0;
}
/**
* The main member function for dispensing pairs of reads or
* singleton reads. Returns true iff ra and rb contain a new
* pair; returns false if ra contains a new unpaired read.
*/
virtual bool nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName);
/**
* Return the number of reads attempted.
*/
virtual pair<TReadId, TReadId> readCnt() const {
uint64_t ret = 0llu;
for(size_t i = 0; i < src_->size(); i++) ret += (*src_)[i]->readCnt();
return make_pair(ret, 0llu);
}
protected:
volatile uint32_t cur_; // current element in parallel srca_, srcb_ vectors
const EList<PatternSource*>* src_; /// PatternSources for paired-end reads
};
/**
* Encapsulates a synchronized source of both paired-end reads and
* unpaired reads, where the paired-end must come from parallel files.
*/
class PairedDualPatternSource : public PairedPatternSource {
public:
PairedDualPatternSource(
const EList<PatternSource*>* srca,
const EList<PatternSource*>* srcb,
const PatternParams& p) :
PairedPatternSource(p), cur_(0), srca_(srca), srcb_(srcb)
{
assert(srca_ != NULL);
assert(srcb_ != NULL);
// srca_ and srcb_ must be parallel
assert_eq(srca_->size(), srcb_->size());
for(size_t i = 0; i < srca_->size(); i++) {
// Can't have NULL first-mate sources. Second-mate sources
// can be NULL, in the case when the corresponding first-
// mate source is unpaired.
assert((*srca_)[i] != NULL);
for(size_t j = 0; j < srcb_->size(); j++) {
assert_neq((*srca_)[i], (*srcb_)[j]);
}
}
}
virtual ~PairedDualPatternSource() {
delete srca_;
delete srcb_;
}
/**
* Call this whenever this PairedPatternSource is wrapped by a new
* WrappedPatternSourcePerThread. This helps us keep track of
* whether locks within PatternSources will be contended.
*/
virtual void addWrapper() {
for(size_t i = 0; i < srca_->size(); i++) {
(*srca_)[i]->addWrapper();
if((*srcb_)[i] != NULL) {
(*srcb_)[i]->addWrapper();
}
}
}
/**
* Reset this object and all the PatternSources under it so that
* the next call to nextReadPair gets the very first read pair.
*/
virtual void reset() {
for(size_t i = 0; i < srca_->size(); i++) {
(*srca_)[i]->reset();
if((*srcb_)[i] != NULL) {
(*srcb_)[i]->reset();
}
}
cur_ = 0;
}
/**
* The main member function for dispensing pairs of reads or
* singleton reads. Returns true iff ra and rb contain a new
* pair; returns false if ra contains a new unpaired read.
*/
virtual bool nextReadPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired,
bool fixName);
/**
* Return the number of reads attempted.
*/
virtual pair<TReadId, TReadId> readCnt() const;
protected:
volatile uint32_t cur_; // current element in parallel srca_, srcb_ vectors
const EList<PatternSource*>* srca_; /// PatternSources for 1st mates and/or unpaired reads
const EList<PatternSource*>* srcb_; /// PatternSources for 2nd mates
};
/**
* Encapsulates a single thread's interaction with the PatternSource.
* Most notably, this class holds the buffers into which the
* PatterSource will write sequences. This class is *not* threadsafe
* - it doesn't need to be since there's one per thread. PatternSource
* is thread-safe.
*/
class PatternSourcePerThread {
public:
PatternSourcePerThread() :
buf1_(), buf2_(), rdid_(0xffffffff), endid_(0xffffffff) { }
virtual ~PatternSourcePerThread() { }
/**
* change 3N plan for both mate1 and mate2
*/
void changePlan3N(int mappingCycle) {
buf1_.changePlan3N(mappingCycle);
buf2_.changePlan3N(3-mappingCycle);
}
/**
* Read the next read pair.
*/
virtual bool nextReadPair(
bool& success,
bool& done,
bool& paired,
bool fixName)
{
return success;
}
Read& bufa() { return buf1_; }
Read& bufb() { return buf2_; }
const Read& bufa() const { return buf1_; }
const Read& bufb() const { return buf2_; }
TReadId rdid() const { return rdid_; }
TReadId endid() const { return endid_; }
virtual void reset() { rdid_ = endid_ = 0xffffffff; }
/**
* Return the length of mate 1 or mate 2.
*/
size_t length(int mate) const {
return (mate == 1) ? buf1_.length() : buf2_.length();
}
protected:
Read buf1_; // read buffer for mate a
Read buf2_; // read buffer for mate b
TReadId rdid_; // index of read just read
TReadId endid_; // index of read just read
};
/**
* Abstract parent factory for PatternSourcePerThreads.
*/
class PatternSourcePerThreadFactory {
public:
virtual ~PatternSourcePerThreadFactory() { }
virtual PatternSourcePerThread* create() const = 0;
virtual EList<PatternSourcePerThread*>* create(uint32_t n) const = 0;
/// Free memory associated with a pattern source
virtual void destroy(PatternSourcePerThread* patsrc) const {
assert(patsrc != NULL);
// Free the PatternSourcePerThread
delete patsrc;
}
/// Free memory associated with a pattern source list
virtual void destroy(EList<PatternSourcePerThread*>* patsrcs) const {
assert(patsrcs != NULL);
// Free all of the PatternSourcePerThreads
for(size_t i = 0; i < patsrcs->size(); i++) {
if((*patsrcs)[i] != NULL) {
delete (*patsrcs)[i];
(*patsrcs)[i] = NULL;
}
}
// Free the vector
delete patsrcs;
}
};
/**
* A per-thread wrapper for a PairedPatternSource.
*/
class WrappedPatternSourcePerThread : public PatternSourcePerThread {
public:
WrappedPatternSourcePerThread(PairedPatternSource& __patsrc) :
patsrc_(__patsrc)
{
patsrc_.addWrapper();
}
/**
* Get the next paired or unpaired read from the wrapped
* PairedPatternSource.
*/
virtual bool nextReadPair(
bool& success,
bool& done,
bool& paired,
bool fixName);
private:
/// Container for obtaining paired reads from PatternSources
PairedPatternSource& patsrc_;
};
/**
* Abstract parent factory for PatternSourcePerThreads.
*/
class WrappedPatternSourcePerThreadFactory : public PatternSourcePerThreadFactory {
public:
WrappedPatternSourcePerThreadFactory(PairedPatternSource& patsrc) :
patsrc_(patsrc) { }
/**
* Create a new heap-allocated WrappedPatternSourcePerThreads.
*/
virtual PatternSourcePerThread* create() const {
return new WrappedPatternSourcePerThread(patsrc_);
}
/**
* Create a new heap-allocated vector of heap-allocated
* WrappedPatternSourcePerThreads.
*/
virtual EList<PatternSourcePerThread*>* create(uint32_t n) const {
EList<PatternSourcePerThread*>* v = new EList<PatternSourcePerThread*>;
for(size_t i = 0; i < n; i++) {
v->push_back(new WrappedPatternSourcePerThread(patsrc_));
assert(v->back() != NULL);
}
return v;
}
private:
/// Container for obtaining paired reads from PatternSources
PairedPatternSource& patsrc_;
};
/// Skip to the end of the current string of newline chars and return
/// the first character after the newline chars, or -1 for EOF
static inline int getOverNewline(FileBuf& in) {
int c;
while(isspace(c = in.get()));
return c;
}
/// Skip to the end of the current string of newline chars such that
/// the next call to get() returns the first character after the
/// whitespace
static inline int peekOverNewline(FileBuf& in) {
while(true) {
int c = in.peek();
if(c != '\r' && c != '\n') {
return c;
}
in.get();
}
}
/// Skip to the end of the current line; return the first character
/// of the next line or -1 for EOF
static inline int getToEndOfLine(FileBuf& in) {
while(true) {
int c = in.get(); if(c < 0) return -1;
if(c == '\n' || c == '\r') {
while(c == '\n' || c == '\r') {
c = in.get(); if(c < 0) return -1;
}
// c now holds first character of next line
return c;
}
}
}
/// Skip to the end of the current line such that the next call to
/// get() returns the first character on the next line
static inline int peekToEndOfLine(FileBuf& in) {
while(true) {
int c = in.get(); if(c < 0) return c;
if(c == '\n' || c == '\r') {
c = in.peek();
while(c == '\n' || c == '\r') {
in.get(); if(c < 0) return c; // consume \r or \n
c = in.peek();
}
// next get() gets first character of next line
return c;
}
}
}
extern void wrongQualityFormat(const BTString& read_name);
extern void tooFewQualities(const BTString& read_name);
extern void tooManyQualities(const BTString& read_name);
/**
* Encapsulates a source of patterns which is an in-memory vector.
*/
class VectorPatternSource : public PatternSource {
public:
VectorPatternSource(
const EList<string>& v,
const PatternParams& p);
virtual ~VectorPatternSource() { }
virtual bool nextReadImpl(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/**
* This is unused, but implementation is given for completeness.
*/
virtual bool nextReadPairImpl(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired);
virtual void reset() {
PatternSource::reset();
cur_ = skip_;
paired_ = false;
}
private:
size_t cur_;
uint32_t skip_;
bool paired_;
EList<BTDnaString> v_; // forward sequences
EList<BTString> quals_; // forward qualities
EList<BTString> names_; // names
EList<int> trimmed3_; // names
EList<int> trimmed5_; // names
};
/**
*
*/
class BufferedFilePatternSource : public PatternSource {
public:
BufferedFilePatternSource(
const EList<string>& infiles,
const PatternParams& p) :
PatternSource(p),
infiles_(infiles),
filecur_(0),
fb_(),
skip_(p.skip),
first_(true)
{
assert_gt(infiles.size(), 0);
errs_.resize(infiles_.size());
errs_.fill(0, infiles_.size(), false);
assert(!fb_.isOpen());
open(); // open first file in the list
filecur_++;
}
virtual ~BufferedFilePatternSource() {
if(fb_.isOpen()) fb_.close();
}
/**
* Fill Read with the sequence, quality and name for the next
* read in the list of read files. This function gets called by
* all the search threads, so we must handle synchronization.
*/
virtual bool nextReadImpl(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
// We'll be manipulating our file handle/filecur_ state
lock();
while(true) {
do { read(r, rdid, endid, success, done); }
while(!success && !done);
if(!success && filecur_ < infiles_.size()) {
assert(done);
open();
resetForNextFile(); // reset state to handle a fresh file
filecur_++;
continue;
}
break;
}
assert(r.repOk());
// Leaving critical region
unlock();
return success;
}
/**
*
*/
virtual bool nextReadPairImpl(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// We'll be manipulating our file handle/filecur_ state
lock();
while(true) {
do { readPair(ra, rb, rdid, endid, success, done, paired); }
while(!success && !done);
if(!success && filecur_ < infiles_.size()) {
assert(done);
open();
resetForNextFile(); // reset state to handle a fresh file
filecur_++;
continue;
}
break;
}
assert(ra.repOk());
assert(rb.repOk());
// Leaving critical region
unlock();
return success;
}
/**
* Reset state so that we read start reading again from the
* beginning of the first file. Should only be called by the
* master thread.
*/
virtual void reset() {
PatternSource::reset();
filecur_ = 0;
open();
filecur_++;
}
protected:
/// Read another pattern from the input file; this is overridden
/// to deal with specific file formats
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done) = 0;
/// Read another pattern pair from the input file; this is
/// overridden to deal with specific file formats
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired) = 0;
/// Reset state to handle a fresh file
virtual void resetForNextFile() { }
void open() {
if(fb_.isOpen()) fb_.close();
while(filecur_ < infiles_.size()) {
// Open read
FILE *in;
if(infiles_[filecur_] == "-") {
in = stdin;
} else if((in = fopen(infiles_[filecur_].c_str(), "rb")) == NULL) {
if(!errs_[filecur_]) {
cerr << "Warning: Could not open read file \"" << infiles_[filecur_].c_str() << "\" for reading; skipping..." << endl;
errs_[filecur_] = true;
}
filecur_++;
continue;
}
fb_.newFile(in);
return;
}
cerr << "Error: No input read files were valid" << endl;
exit(1);
return;
}
EList<string> infiles_; // filenames for read files
EList<bool> errs_; // whether we've already printed an error for each file
size_t filecur_; // index into infiles_ of next file to read
FileBuf fb_; // read file currently being read from
TReadId skip_; // number of reads to skip
bool first_;
};
/**
* Parse a single quality string from fb and store qualities in r.
* Assume the next character obtained via fb.get() is the first
* character of the quality string. When returning, the next
* character returned by fb.peek() or fb.get() should be the first
* character of the following line.
*/
int parseQuals(
Read& r,
FileBuf& fb,
int firstc,
int readLen,
int trim3,
int trim5,
bool intQuals,
bool phred64,
bool solexa64);
/**
* Synchronized concrete pattern source for a list of FASTA or CSFASTA
* (if color = true) files.
*/
class FastaPatternSource : public BufferedFilePatternSource {
public:
FastaPatternSource(const EList<string>& infiles,
const PatternParams& p) :
BufferedFilePatternSource(infiles, p),
first_(true), solexa64_(p.solexa64), phred64_(p.phred64), intQuals_(p.intQuals)
{ }
virtual void reset() {
first_ = true;
BufferedFilePatternSource::reset();
}
protected:
/**
* Scan to the next FASTA record (starting with >) and return the first
* character of the record (which will always be >).
*/
static int skipToNextFastaRecord(FileBuf& in) {
int c;
while((c = in.get()) != '>') {
if(in.eof()) return -1;
}
return c;
}
/// Called when we have to bail without having parsed a read.
void bail(Read& r) {
r.reset();
fb_.resetLastN();
}
/// Read another pattern from a FASTA input file
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/// Read another pair of patterns from a FASTA input file
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// (For now, we shouldn't ever be here)
cerr << "In FastaPatternSource.readPair()" << endl;
throw 1;
return false;
}
virtual void resetForNextFile() {
first_ = true;
}
private:
bool first_;
public:
bool solexa64_;
bool phred64_;
bool intQuals_;
};
/**
* Tokenize a line of space-separated integer quality values.
*/
static inline bool tokenizeQualLine(
FileBuf& filebuf,
char *buf,
size_t buflen,
EList<string>& toks)
{
size_t rd = filebuf.gets(buf, buflen);
if(rd == 0) return false;
assert(NULL == strrchr(buf, '\n'));
tokenize(string(buf), " ", toks);
return true;
}
/**
* Synchronized concrete pattern source for a list of files with tab-
* delimited name, seq, qual fields (or, for paired-end reads,
* basename, seq1, qual1, seq2, qual2).
*/
class TabbedPatternSource : public BufferedFilePatternSource {
public:
TabbedPatternSource(
const EList<string>& infiles,
const PatternParams& p,
bool secondName) :
BufferedFilePatternSource(infiles, p),
solQuals_(p.solexa64),
phred64Quals_(p.phred64),
intQuals_(p.intQuals),
secondName_(secondName) { }
protected:
/// Read another pattern from a FASTA input file
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/// Read another pair of patterns from a FASTA input file
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired);
private:
/**
* Parse a name from fb_ and store in r. Assume that the next
* character obtained via fb_.get() is the first character of
* the sequence and the string stops at the next char upto (could
* be tab, newline, etc.).
*/
int parseName(Read& r, Read* r2, char upto = '\t');
/**
* Parse a single sequence from fb_ and store in r. Assume
* that the next character obtained via fb_.get() is the first
* character of the sequence and the sequence stops at the next
* char upto (could be tab, newline, etc.).
*/
int parseSeq(Read& r, int& charsRead, int& trim5, char upto = '\t');
/**
* Parse a single quality string from fb_ and store in r.
* Assume that the next character obtained via fb_.get() is
* the first character of the quality string and the string stops
* at the next char upto (could be tab, newline, etc.).
*/
int parseQuals(Read& r, int charsRead, int dstLen, int trim5,
char& c2, char upto = '\t', char upto2 = -1);
bool solQuals_;
bool phred64Quals_;
bool intQuals_;
EList<string> qualToks_;
bool secondName_;
};
/**
* Synchronized concrete pattern source for Illumina Qseq files. In
* Qseq files, each read appears on a separate line and the tab-
* delimited fields are:
*
* 1. Machine name
* 2. Run number
* 3. Lane number
* 4. Tile number
* 5. X coordinate of spot
* 6. Y coordinate of spot
* 7. Index: "Index sequence or 0. For no indexing, or for a file that
* has not been demultiplexed yet, this field should have a value of
* 0."
* 8. Read number: 1 for unpaired, 1 or 2 for paired
* 9. Sequence
* 10. Quality
* 11. Filter: 1 = passed, 0 = didn't
*/
class QseqPatternSource : public BufferedFilePatternSource {
public:
QseqPatternSource(
const EList<string>& infiles,
const PatternParams& p) :
BufferedFilePatternSource(infiles, p),
solQuals_(p.solexa64),
phred64Quals_(p.phred64),
intQuals_(p.intQuals) { }
protected:
#define BAIL_UNPAIRED() { \
peekOverNewline(fb_); \
r.reset(); \
success = false; \
done = true; \
return success; \
}
/**
* Parse a name from fb_ and store in r. Assume that the next
* character obtained via fb_.get() is the first character of
* the sequence and the string stops at the next char upto (could
* be tab, newline, etc.).
*/
int parseName(
Read& r, // buffer for mate 1
Read* r2, // buffer for mate 2 (NULL if mate2 is read separately)
bool append, // true -> append characters, false -> skip them
bool clearFirst, // clear the name buffer first
bool warnEmpty, // emit a warning if nothing was added to the name
bool useDefault, // if nothing is read, put readCnt_ as a default value
int upto); // stop parsing when we first reach character 'upto'
/**
* Parse a single sequence from fb_ and store in r. Assume
* that the next character obtained via fb_.get() is the first
* character of the sequence and the sequence stops at the next
* char upto (could be tab, newline, etc.).
*/
int parseSeq(
Read& r, // buffer for read
int& charsRead,
int& trim5,
char upto);
/**
* Parse a single quality string from fb_ and store in r.
* Assume that the next character obtained via fb_.get() is
* the first character of the quality string and the string stops
* at the next char upto (could be tab, newline, etc.).
*/
int parseQuals(
Read& r, // buffer for read
int charsRead,
int dstLen,
int trim5,
char& c2,
char upto,
char upto2);
/**
* Read another pattern from a Qseq input file.
*/
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/**
* Read a pair of patterns from 1 Qseq file. Note: this is never used.
*/
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// (For now, we shouldn't ever be here)
cerr << "In QseqPatternSource.readPair()" << endl;
throw 1;
return false;
}
bool solQuals_;
bool phred64Quals_;
bool intQuals_;
EList<string> qualToks_;
};
/**
* Synchronized concrete pattern source for a list of FASTA files where
* reads need to be extracted from long continuous sequences.
*/
class FastaContinuousPatternSource : public BufferedFilePatternSource {
public:
FastaContinuousPatternSource(const EList<string>& infiles, const PatternParams& p) :
BufferedFilePatternSource(infiles, p),
length_(p.sampleLen), freq_(p.sampleFreq),
eat_(length_-1), beginning_(true),
bufCur_(0), subReadCnt_(0llu)
{
resetForNextFile();
}
virtual void reset() {
BufferedFilePatternSource::reset();
resetForNextFile();
}
protected:
/// Read another pattern from a FASTA input file
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
success = true;
done = false;
r.reset();
while(true) {
r.color = gColor;
int c = fb_.get();
if(c < 0) { success = false; done = true; return success; }
if(c == '>') {
resetForNextFile();
c = fb_.peek();
bool sawSpace = false;
while(c != '\n' && c != '\r') {
if(!sawSpace) {
sawSpace = isspace(c);
}
if(!sawSpace) {
nameBuf_.append(c);
}
fb_.get();
c = fb_.peek();
}
while(c == '\n' || c == '\r') {
fb_.get();
c = fb_.peek();
}
nameBuf_.append('_');
} else {
int cat = asc2dnacat[c];
if(cat >= 2) c = 'N';
if(cat == 0) {
// Encountered non-DNA, non-IUPAC char; skip it
continue;
} else {
// DNA char
buf_[bufCur_++] = c;
if(bufCur_ == 1024) bufCur_ = 0;
if(eat_ > 0) {
eat_--;
// Try to keep readCnt_ aligned with the offset
// into the reference; that lets us see where
// the sampling gaps are by looking at the read
// name
if(!beginning_) readCnt_++;
continue;
}
for(size_t i = 0; i < length_; i++) {
if(length_ - i <= bufCur_) {
c = buf_[bufCur_ - (length_ - i)];
} else {
// Rotate
c = buf_[bufCur_ - (length_ - i) + 1024];
}
r.patFw.append(asc2dna[c]);
r.qual.append('I');
}
// Set up a default name if one hasn't been set
r.name = nameBuf_;
char cbuf[20];
itoa10<TReadId>(readCnt_ - subReadCnt_, cbuf);
r.name.append(cbuf);
eat_ = freq_-1;
readCnt_++;
beginning_ = false;
rdid = endid = readCnt_-1;
break;
}
}
}
return true;
}
/// Shouldn't ever be here; it's not sensible to obtain read pairs
// from a continuous input.
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
cerr << "In FastaContinuousPatternSource.readPair()" << endl;
throw 1;
return false;
}
/**
* Reset state to be read for the next file.
*/
virtual void resetForNextFile() {
eat_ = length_-1;
beginning_ = true;
bufCur_ = 0;
nameBuf_.clear();
subReadCnt_ = readCnt_;
}
private:
size_t length_; /// length of reads to generate
size_t freq_; /// frequency to sample reads
size_t eat_; /// number of characters we need to skip before
/// we have flushed all of the ambiguous or
/// non-existent characters out of our read
/// window
bool beginning_; /// skipping over the first read length?
char buf_[1024]; /// read buffer
BTString nameBuf_; /// read buffer for name of fasta record being
/// split into mers
size_t bufCur_; /// buffer cursor; points to where we should
/// insert the next character
uint64_t subReadCnt_;/// number to subtract from readCnt_ to get
/// the pat id to output (so it resets to 0 for
/// each new sequence)
};
/**
* Read a FASTQ-format file.
* See: http://maq.sourceforge.net/fastq.shtml
*/
class FastqPatternSource : public BufferedFilePatternSource {
public:
FastqPatternSource(const EList<string>& infiles, const PatternParams& p) :
BufferedFilePatternSource(infiles, p),
first_(true),
solQuals_(p.solexa64),
phred64Quals_(p.phred64),
intQuals_(p.intQuals),
fuzzy_(p.fuzzy)
{ }
virtual void reset() {
first_ = true;
fb_.resetLastN();
BufferedFilePatternSource::reset();
}
protected:
/**
* Scan to the next FASTQ record (starting with @) and return the first
* character of the record (which will always be @). Since the quality
* line may start with @, we keep scanning until we've seen a line
* beginning with @ where the line two lines back began with +.
*/
static int skipToNextFastqRecord(FileBuf& in, bool sawPlus) {
int line = 0;
int plusLine = -1;
int c = in.get();
int firstc = c;
while(true) {
if(line > 20) {
// If we couldn't find our desired '@' in the first 20
// lines, it's time to give up
if(firstc == '>') {
// That firstc is '>' may be a hint that this is
// actually a FASTA file, so return it intact
return '>';
}
// Return an error
return -1;
}
if(c == -1) return -1;
if(c == '\n') {
c = in.get();
if(c == '@' && sawPlus && plusLine == (line-2)) {
return '@';
}
else if(c == '+') {
// Saw a '+' at the beginning of a line; remember where
// we saw it
sawPlus = true;
plusLine = line;
}
else if(c == -1) {
return -1;
}
line++;
}
c = in.get();
}
}
/// Read another pattern from a FASTQ input file
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done);
/// Read another read pair from a FASTQ input file
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// (For now, we shouldn't ever be here)
cerr << "In FastqPatternSource.readPair()" << endl;
throw 1;
return false;
}
virtual void resetForNextFile() {
first_ = true;
}
private:
/**
* Do things we need to do if we have to bail in the middle of a
* read, usually because we reached the end of the input without
* finishing.
*/
void bail(Read& r) {
r.patFw.clear();
fb_.resetLastN();
}
bool first_;
bool solQuals_;
bool phred64Quals_;
bool intQuals_;
bool fuzzy_;
EList<string> qualToks_;
};
/**
* Read a Raw-format file (one sequence per line). No quality strings
* allowed. All qualities are assumed to be 'I' (40 on the Phred-33
* scale).
*/
class RawPatternSource : public BufferedFilePatternSource {
public:
RawPatternSource(const EList<string>& infiles, const PatternParams& p) :
BufferedFilePatternSource(infiles, p), first_(true) { }
virtual void reset() {
first_ = true;
BufferedFilePatternSource::reset();
}
protected:
/// Read another pattern from a Raw input file
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
int c;
success = true;
done = false;
r.reset();
c = getOverNewline(this->fb_);
if(c < 0) {
bail(r); success = false; done = true; return success;
}
assert(!isspace(c));
r.color = gColor;
int mytrim5 = gTrim5;
if(first_) {
// Check that the first character is sane for a raw file
int cc = c;
if(gColor) {
if(cc >= '0' && cc <= '4') cc = "ACGTN"[(int)cc - '0'];
if(cc == '.') cc = 'N';
}
if(asc2dnacat[cc] == 0) {
cerr << "Error: reads file does not look like a Raw file" << endl;
if(c == '>') {
cerr << "Reads file looks like a FASTA file; please use -f" << endl;
}
if(c == '@') {
cerr << "Reads file looks like a FASTQ file; please use -q" << endl;
}
throw 1;
}
first_ = false;
}
if(gColor) {
// This may be a primer character. If so, keep it in the
// 'primer' field of the read buf and parse the rest of the
// read without it.
c = toupper(c);
if(asc2dnacat[c] > 0) {
// First char is a DNA char
int c2 = toupper(fb_.peek());
// Second char is a color char
if(asc2colcat[c2] > 0) {
r.primer = c;
r.trimc = c2;
mytrim5 += 2; // trim primer and first color
}
}
if(c < 0) {
bail(r); success = false; done = true; return success;
}
}
// _in now points just past the first character of a sequence
// line, and c holds the first character
int chs = 0;
while(!isspace(c) && c >= 0) {
if(gColor) {
if(c >= '0' && c <= '4') c = "ACGTN"[(int)c - '0'];
if(c == '.') c = 'N';
}
// 5' trimming
if(isalpha(c) && chs >= mytrim5) {
//size_t len = chs - mytrim5;
//if(len >= 1024) tooManyQualities(BTString("(no name)"));
r.patFw.append(asc2dna[c]);
r.qual.append('I');
}
chs++;
if(isspace(fb_.peek())) break;
c = fb_.get();
}
// 3' trimming
r.patFw.trimEnd(gTrim3);
r.qual.trimEnd(gTrim3);
c = peekToEndOfLine(fb_);
r.trimmed3 = gTrim3;
r.trimmed5 = mytrim5;
r.readOrigBuf.install(fb_.lastN(), fb_.lastNLen());
fb_.resetLastN();
// Set up name
char cbuf[20];
itoa10<TReadId>(readCnt_, cbuf);
r.name.install(cbuf);
readCnt_++;
rdid = endid = readCnt_-1;
return success;
}
/// Read another read pair from a FASTQ input file
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// (For now, we shouldn't ever be here)
cerr << "In RawPatternSource.readPair()" << endl;
throw 1;
return false;
}
virtual void resetForNextFile() {
first_ = true;
}
private:
/**
* Do things we need to do if we have to bail in the middle of a
* read, usually because we reached the end of the input without
* finishing.
*/
void bail(Read& r) {
r.patFw.clear();
fb_.resetLastN();
}
bool first_;
};
#ifdef USE_SRA
namespace ngs {
class ReadCollection;
class ReadIterator;
}
namespace tthread {
class thread;
};
struct SRA_Data;
/**
*
*/
class SRAPatternSource : public PatternSource {
public:
SRAPatternSource(
const EList<string>& sra_accs,
const PatternParams& p,
const size_t nthreads = 1) :
PatternSource(p),
sra_accs_(sra_accs),
sra_acc_cur_(0),
skip_(p.skip),
first_(true),
nthreads_(nthreads),
sra_run_(NULL),
sra_it_(NULL),
sra_data_(NULL),
io_thread_(NULL)
{
assert_gt(sra_accs_.size(), 0);
errs_.resize(sra_accs_.size());
errs_.fill(0, sra_accs_.size(), false);
open(); // open first file in the list
sra_acc_cur_++;
}
virtual ~SRAPatternSource();
/**
* Fill Read with the sequence, quality and name for the next
* read in the list of read files. This function gets called by
* all the search threads, so we must handle synchronization.
*/
virtual bool nextReadImpl(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
// We'll be manipulating our file handle/filecur_ state
lock();
while(true) {
do { read(r, rdid, endid, success, done); }
while(!success && !done);
if(!success && sra_acc_cur_ < sra_accs_.size()) {
assert(done);
open();
resetForNextFile(); // reset state to handle a fresh file
sra_acc_cur_++;
continue;
}
break;
}
assert(r.repOk());
// Leaving critical region
unlock();
return success;
}
/**
*
*/
virtual bool nextReadPairImpl(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired)
{
// We'll be manipulating our file handle/filecur_ state
lock();
while(true) {
do { readPair(ra, rb, rdid, endid, success, done, paired); }
while(!success && !done);
if(!success && sra_acc_cur_ < sra_accs_.size()) {
assert(done);
open();
resetForNextFile(); // reset state to handle a fresh file
sra_acc_cur_++;
continue;
}
break;
}
assert(ra.repOk());
assert(rb.repOk());
// Leaving critical region
unlock();
return success;
}
/**
* Reset state so that we read start reading again from the
* beginning of the first file. Should only be called by the
* master thread.
*/
virtual void reset() {
PatternSource::reset();
sra_acc_cur_ = 0,
open();
sra_acc_cur_++;
}
/// Read another pattern from the input file; this is overridden
/// to deal with specific file formats
virtual bool read(
Read& r,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done)
{
return true;
}
/// Read another pattern pair from the input file; this is
/// overridden to deal with specific file formats
virtual bool readPair(
Read& ra,
Read& rb,
TReadId& rdid,
TReadId& endid,
bool& success,
bool& done,
bool& paired);
protected:
/// Reset state to handle a fresh file
virtual void resetForNextFile() { }
void open();
EList<string> sra_accs_; // filenames for read files
EList<bool> errs_; // whether we've already printed an error for each file
size_t sra_acc_cur_; // index into infiles_ of next file to read
TReadId skip_; // number of reads to skip
bool first_;
size_t nthreads_;
ngs::ReadCollection* sra_run_;
ngs::ReadIterator* sra_it_;
SRA_Data* sra_data_;
tthread::thread* io_thread_;
};
#endif
#endif /*PAT_H_*/
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