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centrifuge_compress.cpp
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centrifuge_compress.cpp
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/*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of Centrifuge.
*
* Centrifuge 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.
*
* Centrifuge 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 Centrifuge. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
#include <fstream>
#include <string>
#include <cassert>
#include <getopt.h>
#include "assert_helpers.h"
#include "endian_swap.h"
#include "bt2_idx.h"
#include "bt2_io.h"
#include "bt2_util.h"
#include "formats.h"
#include "sequence_io.h"
#include "tokenize.h"
#include "timer.h"
#include "ref_read.h"
#include "filebuf.h"
#include "reference.h"
#include "ds.h"
#include "aligner_sw.h"
/**
* \file Driver for the bowtie-build indexing tool.
*/
// Build parameters
int verbose;
static int sanityCheck;
static int format;
static TIndexOffU bmax;
static TIndexOffU bmaxMultSqrt;
static uint32_t bmaxDivN;
static int dcv;
static int noDc;
static int entireSA;
static int seed;
static int showVersion;
// Ebwt parameters
static int32_t lineRate;
static int32_t linesPerSide;
static int32_t offRate;
static int32_t ftabChars;
static int32_t localOffRate;
static int32_t localFtabChars;
static int bigEndian;
static bool nsToAs;
static bool doSaFile; // make a file with just the suffix array in it
static bool doBwtFile; // make a file with just the BWT string in it
static bool autoMem;
static bool packed;
static bool writeRef;
static bool justRef;
static bool reverseEach;
static string wrapper;
static int across;
static size_t minSimLen; // minimum similar length
static bool printN;
static void resetOptions() {
verbose = true; // be talkative (default)
sanityCheck = 0; // do slow sanity checks
format = FASTA; // input sequence format
bmax = OFF_MASK; // max blockwise SA bucket size
bmaxMultSqrt = OFF_MASK; // same, as multplier of sqrt(n)
bmaxDivN = 4; // same, as divisor of n
dcv = 1024; // bwise SA difference-cover sample sz
noDc = 0; // disable difference-cover sample
entireSA = 0; // 1 = disable blockwise SA
seed = 0; // srandom seed
showVersion = 0; // just print version and quit?
// Ebwt parameters
lineRate = Ebwt<TIndexOffU>::default_lineRate;
linesPerSide = 1; // 1 64-byte line on a side
offRate = 4; // sample 1 out of 16 SA elts
ftabChars = 10; // 10 chars in initial lookup table
localOffRate = 3;
localFtabChars = 6;
bigEndian = 0; // little endian
nsToAs = false; // convert reference Ns to As prior to indexing
doSaFile = false; // make a file with just the suffix array in it
doBwtFile = false; // make a file with just the BWT string in it
autoMem = true; // automatically adjust memory usage parameters
packed = false; //
writeRef = true; // write compact reference to .3.bt2/.4.bt2
justRef = false; // *just* write compact reference, don't index
reverseEach = false;
across = 60; // number of characters across in FASTA output
minSimLen = 100;
printN = false;
wrapper.clear();
}
// Argument constants for getopts
enum {
ARG_BMAX = 256,
ARG_BMAX_MULT,
ARG_BMAX_DIV,
ARG_DCV,
ARG_SEED,
ARG_CUTOFF,
ARG_PMAP,
ARG_NTOA,
ARG_USAGE,
ARG_REVERSE_EACH,
ARG_SA,
ARG_WRAPPER,
ARG_LOCAL_OFFRATE,
ARG_LOCAL_FTABCHARS,
ARG_MIN_SIMLEN,
ARG_PRINTN,
};
/**
* Print a detailed usage message to the provided output stream.
*/
static void printUsage(ostream& out) {
out << "Centrifuge version " << string(CENTRIFUGE_VERSION).c_str() << " by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)" << endl;
#ifdef BOWTIE_64BIT_INDEX
string tool_name = "hisat-build-l";
#else
string tool_name = "hisat-build-s";
#endif
if(wrapper == "basic-0") {
tool_name = "hisat-build";
}
out << "Usage: hisat2-build [options]* <reference_in> <bt2_index_base>" << endl
<< " reference_in comma-separated list of files with ref sequences" << endl
<< " hisat_index_base write " << gEbwt_ext << " data to files with this dir/basename" << endl
<< "Options:" << endl
<< " -c reference sequences given on cmd line (as" << endl
<< " <reference_in>)" << endl;
if(wrapper == "basic-0") {
out << " --large-index force generated index to be 'large', even if ref" << endl
<< " has fewer than 4 billion nucleotides" << endl;
}
out << " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting" << endl
<< " -p/--packed use packed strings internally; slower, uses less mem" << endl
<< " --bmax <int> max bucket sz for blockwise suffix-array builder" << endl
<< " --bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)" << endl
<< " --dcv <int> diff-cover period for blockwise (default: 1024)" << endl
<< " --nodc disable diff-cover (algorithm becomes quadratic)" << endl
<< " -r/--noref don't build .3/.4.bt2 (packed reference) portion" << endl
<< " -3/--justref just build .3/.4.bt2 (packed reference) portion" << endl
<< " -o/--offrate <int> SA is sampled every 2^offRate BWT chars (default: 5)" << endl
<< " -t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)" << endl
<< " --localoffrate <int> SA (local) is sampled every 2^offRate BWT chars (default: 3)" << endl
<< " --localftabchars <int> # of chars consumed in initial lookup in a local index (default: 6)" << endl
<< " --seed <int> seed for random number generator" << endl
<< " -q/--quiet verbose output (for debugging)" << endl
<< " --printN print original sequence with mask" << endl
<< " -h/--help print detailed description of tool and its options" << endl
<< " --usage print this usage message" << endl
<< " --version print version information and quit" << endl
;
if(wrapper.empty()) {
cerr << endl
<< "*** Warning ***" << endl
<< "'" << tool_name << "' was run directly. It is recommended "
<< "that you run the wrapper script 'bowtie2-build' instead."
<< endl << endl;
}
}
static const char *short_options = "qraph?nscfl:i:o:t:h:3C";
static struct option long_options[] = {
{(char*)"quiet", no_argument, 0, 'q'},
{(char*)"sanity", no_argument, 0, 's'},
{(char*)"packed", no_argument, 0, 'p'},
{(char*)"little", no_argument, &bigEndian, 0},
{(char*)"big", no_argument, &bigEndian, 1},
{(char*)"bmax", required_argument, 0, ARG_BMAX},
{(char*)"bmaxmultsqrt", required_argument, 0, ARG_BMAX_MULT},
{(char*)"bmaxdivn", required_argument, 0, ARG_BMAX_DIV},
{(char*)"dcv", required_argument, 0, ARG_DCV},
{(char*)"nodc", no_argument, &noDc, 1},
{(char*)"seed", required_argument, 0, ARG_SEED},
{(char*)"entiresa", no_argument, &entireSA, 1},
{(char*)"version", no_argument, &showVersion, 1},
{(char*)"noauto", no_argument, 0, 'a'},
{(char*)"noblocks", required_argument, 0, 'n'},
{(char*)"linerate", required_argument, 0, 'l'},
{(char*)"linesperside", required_argument, 0, 'i'},
{(char*)"offrate", required_argument, 0, 'o'},
{(char*)"ftabchars", required_argument, 0, 't'},
{(char*)"localoffrate", required_argument, 0, ARG_LOCAL_OFFRATE},
{(char*)"localftabchars", required_argument, 0, ARG_LOCAL_FTABCHARS},
{(char*)"help", no_argument, 0, 'h'},
{(char*)"ntoa", no_argument, 0, ARG_NTOA},
{(char*)"justref", no_argument, 0, '3'},
{(char*)"noref", no_argument, 0, 'r'},
{(char*)"color", no_argument, 0, 'C'},
{(char*)"sa", no_argument, 0, ARG_SA},
{(char*)"reverse-each", no_argument, 0, ARG_REVERSE_EACH},
{(char*)"min-simlen", required_argument, 0, ARG_MIN_SIMLEN},
{(char*)"printN", no_argument, 0, ARG_PRINTN},
{(char*)"usage", no_argument, 0, ARG_USAGE},
{(char*)"wrapper", required_argument, 0, ARG_WRAPPER},
{(char*)0, 0, 0, 0} // terminator
};
/**
* Parse an int out of optarg and enforce that it be at least 'lower';
* if it is less than 'lower', then output the given error message and
* exit with an error and a usage message.
*/
template<typename T>
static int parseNumber(T lower, const char *errmsg) {
char *endPtr= NULL;
T t = (T)strtoll(optarg, &endPtr, 10);
if (endPtr != NULL) {
if (t < lower) {
cerr << errmsg << endl;
printUsage(cerr);
throw 1;
}
return t;
}
cerr << errmsg << endl;
printUsage(cerr);
throw 1;
return -1;
}
/**
* Read command-line arguments
*/
static void parseOptions(int argc, const char **argv) {
int option_index = 0;
int next_option;
do {
next_option = getopt_long(
argc, const_cast<char**>(argv),
short_options, long_options, &option_index);
switch (next_option) {
case ARG_WRAPPER:
wrapper = optarg;
break;
case 'f': format = FASTA; break;
case 'c': format = CMDLINE; break;
case 'p': packed = true; break;
case 'C':
cerr << "Error: -C specified but Bowtie 2 does not support colorspace input." << endl;
throw 1;
break;
case 'l':
lineRate = parseNumber<int>(3, "-l/--lineRate arg must be at least 3");
break;
case 'i':
linesPerSide = parseNumber<int>(1, "-i/--linesPerSide arg must be at least 1");
break;
case 'o':
offRate = parseNumber<int>(0, "-o/--offRate arg must be at least 0");
break;
case ARG_LOCAL_OFFRATE:
localOffRate = parseNumber<int>(0, "-o/--localoffrate arg must be at least 0");
break;
case '3':
justRef = true;
break;
case 't':
ftabChars = parseNumber<int>(1, "-t/--ftabChars arg must be at least 1");
break;
case ARG_LOCAL_FTABCHARS:
localFtabChars = parseNumber<int>(1, "-t/--localftabchars arg must be at least 1");
break;
case 'n':
// all f-s is used to mean "not set", so put 'e' on end
bmax = 0xfffffffe;
break;
case 'h':
case ARG_USAGE:
printUsage(cout);
throw 0;
break;
case ARG_BMAX:
bmax = parseNumber<TIndexOffU>(1, "--bmax arg must be at least 1");
bmaxMultSqrt = OFF_MASK; // don't use multSqrt
bmaxDivN = 0xffffffff; // don't use multSqrt
break;
case ARG_BMAX_MULT:
bmaxMultSqrt = parseNumber<TIndexOffU>(1, "--bmaxmultsqrt arg must be at least 1");
bmax = OFF_MASK; // don't use bmax
bmaxDivN = 0xffffffff; // don't use multSqrt
break;
case ARG_BMAX_DIV:
bmaxDivN = parseNumber<uint32_t>(1, "--bmaxdivn arg must be at least 1");
bmax = OFF_MASK; // don't use bmax
bmaxMultSqrt = OFF_MASK; // don't use multSqrt
break;
case ARG_DCV:
dcv = parseNumber<int>(3, "--dcv arg must be at least 3");
break;
case ARG_SEED:
seed = parseNumber<int>(0, "--seed arg must be at least 0");
break;
case ARG_REVERSE_EACH:
reverseEach = true;
break;
case ARG_SA:
doSaFile = true;
break;
case ARG_NTOA: nsToAs = true; break;
case ARG_MIN_SIMLEN:
minSimLen = parseNumber<size_t>(2, "--min-simlen arg must be at least 2");
break;
case ARG_PRINTN: printN = true; break;
case 'a': autoMem = false; break;
case 'q': verbose = false; break;
case 's': sanityCheck = true; break;
case 'r': writeRef = false; break;
case -1: /* Done with options. */
break;
case 0:
if (long_options[option_index].flag != 0)
break;
default:
printUsage(cerr);
throw 1;
}
} while(next_option != -1);
if(bmax < 40) {
cerr << "Warning: specified bmax is very small (" << bmax << "). This can lead to" << endl
<< "extremely slow performance and memory exhaustion. Perhaps you meant to specify" << endl
<< "a small --bmaxdivn?" << endl;
}
}
EList<string> filesWritten;
static void print_fasta_record(
ostream& fout,
const string& defline,
const SString<char>& seq,
size_t len)
{
fout << ">";
fout << defline.c_str() << endl;
if(across > 0) {
size_t i = 0;
while (i + across < len)
{
for(size_t j = 0; j < (unsigned)across; j++) {
int base = seq.get(i + j);
assert_lt(base, 4);
fout << "ACGTN"[base];
}
fout << endl;
i += across;
}
if (i < len) {
for(size_t j = i; j < len; j++) {
int base = seq.get(j);
assert_lt(base, 4);
fout << "ACGTN"[base];
}
fout << endl;
}
} else {
for(size_t j = 0; j < len; j++) {
int base = seq.get(j);
assert_lt(base, 4);
fout << "ACGTN"[base];
}
fout << endl;
}
}
struct RegionSimilar {
bool fw;
size_t pos;
uint32_t fw_length; // this includes the base at 'pos'
uint32_t bw_length;
uint32_t mismatches;
uint32_t gaps;
void reset() {
fw = false;
pos = 0;
fw_length = bw_length = 0;
mismatches = gaps = 0;
}
bool operator< (const RegionSimilar& o) const {
return pos < o.pos;
}
};
struct Region {
size_t pos;
uint32_t fw_length;
uint32_t bw_length; // used for merging
bool low_complexity;
uint32_t match_begin;
uint32_t match_end;
uint32_t match_size() {
assert_leq(match_begin, match_end);
return match_end - match_begin;
}
void reset() {
pos = fw_length = bw_length = 0, low_complexity = false;
match_begin = match_end = 0;
}
bool operator< (const Region& o) const {
return pos < o.pos;
}
};
struct RegionToMerge {
bool processed;
EList<pair<uint32_t, uint32_t> > list;
void reset() {
processed = false;
list.clear();
}
};
/**
* Drive the index construction process and optionally sanity-check the
* result.
*/
static void driver(
const string& fafile,
const string& safile,
bool packed,
int reverse)
{
EList<FileBuf*> is(MISC_CAT);
bool bisulfite = false;
RefReadInParams refparams(false, reverse, nsToAs, bisulfite);
FILE *f = fopen(fafile.c_str(), "r");
if (f == NULL) {
cerr << "Error: could not open "<<fafile.c_str() << endl;
throw 1;
}
FileBuf *fb = new FileBuf(f);
assert(fb != NULL);
if(fb->peek() == -1 || fb->eof()) {
cerr << "Warning: Empty fasta file: '" << fafile.c_str() << "'" << endl;
throw 1;
}
assert(!fb->eof());
assert(fb->get() == '>');
ASSERT_ONLY(fb->reset());
assert(!fb->eof());
is.push_back(fb);
if(is.empty()) {
cerr << "Warning: All fasta inputs were empty" << endl;
throw 1;
}
// Vector for the ordered list of "records" comprising the input
// sequences. A record represents a stretch of unambiguous
// characters in one of the input sequences.
EList<RefRecord> szs(MISC_CAT);
BitPairReference::szsFromFasta(is, string(), bigEndian, refparams, szs, sanityCheck);
assert_gt(szs.size(), 0);
EList<string> refnames;
SString<char> s;
assert_eq(szs.size(), 1);
size_t jlen = szs[0].len;
try {
Timer _t(cerr, " (1/5) Time reading reference sequence: ", verbose);
s.resize(jlen);
RefReadInParams rpcp = refparams;
// For each filebuf
assert_eq(is.size(), 1);
FileBuf *fb = is[0];
assert(!fb->eof());
// For each *fragment* (not necessary an entire sequence) we
// can pull out of istream l[i]...
if(!fb->eof()) {
// Push a new name onto our vector
refnames.push_back("");
TIndexOffU distoff = 0;
fastaRefReadAppend(*fb, true, s, distoff, rpcp, &refnames.back());
}
fb->reset();
assert(!fb->eof());
// Joined reference sequence now in 's'
} catch(bad_alloc& e) {
// If we throw an allocation exception in the try block,
// that means that the joined version of the reference
// string itself is too larger to fit in memory. The only
// alternatives are to tell the user to give us more memory
// or to try again with a packed representation of the
// reference (if we haven't tried that already).
cerr << "Could not allocate space for a joined string of " << jlen << " elements." << endl;
// There's no point passing this exception on. The fact
// that we couldn't allocate the joined string means that
// --bmax is irrelevant - the user should re-run with
// ebwt-build-packed
if(packed) {
cerr << "Please try running bowtie-build on a computer with more memory." << endl;
} else {
cerr << "Please try running bowtie-build in packed mode (-p/--packed) or in automatic" << endl
<< "mode (-a/--auto), or try again on a computer with more memory." << endl;
}
if(sizeof(void*) == 4) {
cerr << "If this computer has more than 4 GB of memory, try using a 64-bit executable;" << endl
<< "this executable is 32-bit." << endl;
}
throw 1;
}
// Succesfully obtained joined reference string
assert_eq(s.length(), jlen);
size_t sense_seq_len = s.length();
size_t both_seq_len = sense_seq_len * 2;
assert_geq(sense_seq_len, 2);
SwAligner sw;
SimpleFunc scoreMin; scoreMin.init(SIMPLE_FUNC_LINEAR, DEFAULT_MIN_CONST, DEFAULT_MIN_LINEAR);
SimpleFunc nCeil; nCeil.init(SIMPLE_FUNC_LINEAR, 0.0f, std::numeric_limits<double>::max(), 2.0f, 0.1f);
const int gGapBarrier = 4;
Scoring sc(
DEFAULT_MATCH_BONUS, // constant reward for match
DEFAULT_MATCH_BONUS_TYPE, // how to penalize mismatches
DEFAULT_MM_PENALTY_MAX, // max mm pelanty
DEFAULT_MM_PENALTY_MIN, // min mm pelanty
scoreMin, // min score as function of read len
nCeil, // max # Ns as function of read len
DEFAULT_N_PENALTY_TYPE, // how to penalize Ns in the read
DEFAULT_N_PENALTY, // constant if N pelanty is a constant
DEFAULT_N_CAT_PAIR, // whether to concat mates before N filtering
DEFAULT_READ_GAP_CONST, // constant coeff for read gap cost
DEFAULT_REF_GAP_CONST, // constant coeff for ref gap cost
DEFAULT_READ_GAP_LINEAR, // linear coeff for read gap cost
DEFAULT_REF_GAP_LINEAR, // linear coeff for ref gap cost
gGapBarrier); // # rows at top/bot only entered diagonally
size_t tmp_sense_seq_len = sense_seq_len;
size_t min_kmer = 0;
while(tmp_sense_seq_len > 0) {
tmp_sense_seq_len >>= 2;
min_kmer++;
}
//
min_kmer += 4;
const size_t min_seed_length = min_kmer * 2;
//
min_kmer += 10;
EList<Region> regions;
EList<RegionSimilar> regions_similar;
{
EList<size_t> sa;
EList<uint16_t> prefix_lengths;
prefix_lengths.resizeExact(sense_seq_len);
prefix_lengths.fillZero();
{
Timer _t(cerr, " (2/5) Time finding seeds using suffix array and reference sequence: ", verbose);
ifstream in(safile.c_str(), ios::binary);
const size_t sa_size = readIndex<uint64_t>(in, false);
#if 0
for(size_t i = 0; i < sa_size; i++) {
size_t pos = (size_t)readIndex<uint64_t>(in, false);
if(pos == sa_size) continue;
size_t opos = both_seq_len - pos - 1;
size_t cpos = min(pos, opos);
bool fw = pos == cpos;
cout << i << " ";
for(size_t j = 0; j < 20; j++) {
int base = 0;
if(fw) {
if(pos + j >= sense_seq_len) break;
base = s[pos+j];
} else {
if(cpos < j) break;
base = 3 - s[cpos-j];
}
cout << "ACGT"[base];
}
cout << " " << pos << endl;
}
exit(1);
#endif
assert_eq(both_seq_len + 1, sa_size);
size_t sa_begin = 0, sa_end = 0;
// Compress sequences by removing redundant sub-sequences
size_t last_i1 = 0;
for(size_t i1 = 0; i1 < sa_size - 1; i1++) {
// daehwan - for debugging purposes
if((i1 + 1) % 1000000 == 0) {
cerr << "\t\t" << (i1 + 1) / 1000000 << " million" << endl;
}
if(i1 >= sa_end) {
assert_leq(sa_begin, sa_end);
assert_eq(i1, sa_end);
size_t sa_pos = (size_t)readIndex<uint64_t>(in, false);
sa.push_back(sa_pos);
sa_end++;
assert_eq(sa_end - sa_begin, sa.size());
}
assert_geq(i1, sa_begin); assert_lt(i1, sa_end);
size_t pos1 = sa[i1-sa_begin];
if(pos1 == both_seq_len) continue;
if(pos1 + min_seed_length >= sense_seq_len) continue;
// Compare with the following sequences
bool expanded = false;
size_t i2 = last_i1 + 1;
for(; i2 < sa_size; i2++) {
if(i1 == i2) continue;
if(i2 >= sa_end) {
assert_leq(sa_begin, sa_end);
assert_eq(i2, sa_end);
size_t sa_pos = (size_t)readIndex<uint64_t>(in, false);
sa.push_back(sa_pos);
sa_end++;
assert_eq(sa_end - sa_begin, sa.size());
}
assert_geq(i2, sa_begin); assert_lt(i2, sa_end);
size_t pos2 = sa[i2-sa_begin];
if(pos2 == both_seq_len) continue;
// opos2 is relative pos of pos2 on the other strand
size_t opos2 = both_seq_len - pos2 - 1;
// cpos2 is canonical pos on the sense strand
size_t cpos2 = min(pos2, opos2);
bool fw = pos2 == cpos2;
if(fw) {
if(pos2 + min_kmer > sense_seq_len) continue;
} else {
if(pos2 + min_kmer > both_seq_len) continue;
}
size_t j1 = 0; // includes the base at 'pos1'
while(pos1 + j1 < sense_seq_len && pos2 + j1 < (fw ? sense_seq_len : both_seq_len)) {
if(!fw) {
if(pos1 < cpos2 && pos1 + (j1 * 2) >= cpos2) break;
}
int base1 = s[pos1 + j1];
int base2;
if(fw) {
base2 = s[pos2 + j1];
} else {
assert_geq(cpos2, j1);
base2 = 3 - s[cpos2 - j1];
}
if(base1 > 3 || base2 > 3) break;
if(base1 != base2) break;
j1++;
}
if(j1 < min_kmer) {
if(i2 > i1) break;
else continue;
}
size_t j2 = 0; // doesn't include the base at 'pos1'
while(j2 <= pos1 && (fw ? 0 : sense_seq_len) + j2 <= pos2) {
if(!fw) {
if(cpos2 < pos1 && cpos2 + (j2 * 2) >= pos1) break;
}
int base1 = s[pos1 - j2];
int base2;
if(fw) {
base2 = s[pos2 - j2];
} else {
assert_lt(cpos2 + j2, s.length());
base2 = 3 - s[cpos2 + j2];
}
if(base1 > 3 || base2 > 3) break;
if(base1 != base2) break;
j2++;
}
if(j2 > 0) j2--;
size_t j = j1 + j2;
// Do not proceed if two sequences are not similar
if(j < min_seed_length) continue;
assert_leq(pos1 + j1, prefix_lengths.size());
if(!expanded && j1 <= prefix_lengths[pos1]) continue;
if(!expanded) {
regions.expand();
regions.back().reset();
regions.back().pos = pos1;
regions.back().fw_length = j1;
regions.back().match_begin = regions.back().match_end = regions_similar.size();
for(size_t k = 0; k < j1; k++) {
size_t tmp_length = j1 - k;
if(prefix_lengths[pos1 + k] < tmp_length) {
prefix_lengths[pos1 + k] = tmp_length;
}
}
expanded = true;
}
if(regions.back().fw_length < j1) {
regions.back().fw_length = j1;
}
regions_similar.expand();
regions_similar.back().reset();
regions_similar.back().fw = fw;
regions_similar.back().pos = cpos2;
if(fw) {
regions_similar.back().fw_length = j1;
regions_similar.back().bw_length = j2;
} else {
regions_similar.back().fw_length = j1 > 0 ? j2 + 1 : 0;
regions_similar.back().bw_length = j1 > 0 ? j1 - 1 : 0;
}
regions.back().match_end = regions_similar.size();
if(regions.back().match_size() >= 20) break;
}
last_i1 = i1;
assert_geq(last_i1, sa_begin);
if(last_i1 >= sa_begin + 1024) {
assert_lt(last_i1, sa_end);
sa.erase(0, last_i1 - sa_begin);
sa_begin = last_i1;
assert_eq(sa_end - sa_begin, sa.size());
}
if(expanded) {
assert_gt(regions.size(), 0);
assert_lt(regions.back().match_begin, regions.back().match_end);
assert_eq(regions.back().match_end, regions_similar.size());
if(regions.back().match_size() > 1) {
regions_similar.sortPortion(regions.back().match_begin, regions.back().match_size());
size_t cur_pos = regions.back().match_begin + 1;
for(size_t i = regions.back().match_begin + 1; i < regions.back().match_end; i++) {
assert_gt(cur_pos, 0);
const RegionSimilar& last_region = regions_similar[cur_pos-1];
const RegionSimilar& new_region = regions_similar[i];
if(last_region.fw == new_region.fw) {
if(last_region.fw) {
if(last_region.pos + last_region.fw_length >= new_region.pos) {
continue;
}
} else {
if(last_region.pos + last_region.fw_length >= new_region.pos) {
regions_similar[cur_pos-1] = new_region;
continue;
}
}
}
if(cur_pos != i) {
assert_lt(cur_pos, regions_similar.size());
regions_similar[cur_pos] = new_region;
}
cur_pos++;
}
if(cur_pos < regions.back().match_end) {
regions.back().low_complexity = true;
}
regions_similar.resize(cur_pos);
regions.back().match_end = regions_similar.size();
}
}
// daehwan - for debugging purposes
#if 1
assert_lt(i1, i2);
if(i1 + 8 < i2) {
i1 = i1 + (i2 - i1) / 2;
}
#endif
}
}
{
Timer _t(cerr, " (3/5) Time sorting seeds and then removing redundant seeds: ", verbose);
regions.sort();
if(regions.size() > 1) {
size_t cur_pos = 1;
for(size_t i = 1; i < regions.size(); i++) {
assert_gt(cur_pos, 0);
const Region& last_region = regions[cur_pos-1];
const Region& new_region = regions[i];
if(last_region.low_complexity && last_region.pos + last_region.fw_length > new_region.pos) continue;
if(last_region.pos + last_region.fw_length >= new_region.pos + new_region.fw_length) continue;
if(cur_pos != i) {
assert_lt(cur_pos, regions.size());
regions[cur_pos] = new_region;
}
cur_pos++;
}
regions.resizeExact(cur_pos);
}
}
}
// Print regions
#if 0
cout << "no. of regions: " << regions.size() << endl << endl;
for(size_t i = 0; i < regions.size(); i++) {
const Region& region = regions[i];
cout << "At " << region.pos << "\t" << region.fw_length << " bps" << endl;
for(size_t j = 0; j < region.hits.size(); j++) {
const RegionSimilar& region2 = region.hits[j];
cout << "\t" << (region2.fw ? "+" : "-") << "\tat " << region2.pos
<< "\t-" << region2.bw_length
<< "\t+" << region2.fw_length << endl;
}
cout << endl << endl;
}
#endif
const size_t min_sim_length = minSimLen;
{
Timer _t(cerr, " (4/5) Time merging seeds and masking sequence: ", verbose);
EList<uint8_t> mask;
mask.resizeExact(sense_seq_len);
mask.fillZero();
EList<RegionToMerge> merge_list;
for(size_t i = 0; i < regions.size(); i++) {
const Region& region = regions[i];
if(i == 0) {
for(size_t j = region.match_begin; j < region.match_end; j++) {
merge_list.expand();
merge_list.back().reset();
merge_list.back().list.expand();
merge_list.back().list.back().first = i;
merge_list.back().list.back().second = j;
}
} else {
assert_gt(i, 0);
for(size_t j = region.match_begin; j < region.match_end; j++) {
assert_lt(j, regions_similar.size());
const RegionSimilar& cmp_region = regions_similar[j];
bool added = false;
for(size_t k = 0; k < merge_list.size(); k++) {
RegionToMerge& merge = merge_list[k];
uint32_t region_id1 = merge.list.back().first;
if(region_id1 >= i) break;
uint32_t region_id2 = merge.list.back().second;
assert_lt(region_id1, regions.size());
const Region& prev_region = regions[region_id1];
assert_lt(region_id2, regions_similar.size());
assert_lt(prev_region.pos, region.pos);
size_t gap = region.pos - prev_region.pos;
const RegionSimilar& prev_cmp_region = regions_similar[region_id2];
if(prev_cmp_region.fw != cmp_region.fw) continue;
if(prev_cmp_region.pos + cmp_region.bw_length == cmp_region.pos + prev_cmp_region.bw_length &&
prev_cmp_region.pos + prev_cmp_region.fw_length == cmp_region.pos + cmp_region.fw_length)
continue;
if(!cmp_region.fw) {
if(cmp_region.pos >= prev_region.pos && cmp_region.pos < region.pos) continue;
}
size_t cmp_gap = 0;
if(cmp_region.fw) {
if(prev_cmp_region.pos >= cmp_region.pos) continue;
cmp_gap = cmp_region.pos - prev_cmp_region.pos;
} else {
if(prev_cmp_region.pos <= cmp_region.pos) continue;
cmp_gap = prev_cmp_region.pos - cmp_region.pos;
}
if(cmp_gap + 10 < gap || gap + 10 < cmp_gap) continue;
if(prev_region.fw_length + 200 < gap) continue;
if(cmp_region.fw) {
if(prev_cmp_region.fw_length + 200 < cmp_gap) continue;
} else {
if(cmp_region.fw_length + 200 < cmp_gap) continue;
}
added = true;
merge.list.expand();
merge.list.back().first = i;
merge.list.back().second = j;
}
if(!added) {
added = true;
merge_list.expand();
merge_list.back().reset();
merge_list.back().list.expand();
merge_list.back().list.back().first = i;
merge_list.back().list.back().second = j;
}
}
}
for(size_t j = 0; j < merge_list.size(); j++) {
RegionToMerge& merge = merge_list[j];
uint32_t region_id1 = merge.list.back().first;
if(i + 1 < regions.size()) {
if(region_id1 == i) continue;
assert_lt(region_id1, regions.size());
const Region& prev_region = regions[region_id1];
if(prev_region.pos + 200 > region.pos) continue;
}
merge_list[j].processed = true;
#if 0
bool skip_merge = true;
for(size_t k = 0; k < merge.list.size(); k++) {
uint32_t region_id1 = merge.list[k].first;
uint32_t region_id2 = merge.list[k].second;
assert_lt(region_id1, regions.size());
const Region& region = regions[region_id1];
assert_lt(region_id2, region.hits.size());
const RegionSimilar& sim_region = region.hits[region_id2];
assert_lt(region.pos, mask.size()); assert_lt(sim_region.pos, mask.size());
if(mask[region.pos] == 0 || mask[sim_region.pos] == 0) {
skip_merge = false;
break;
}
}
if(skip_merge) continue;
#endif
#if 0
bool output_merge = merge.list.size() > 1;
if(!output_merge) {
assert_gt(merge.list.size(), 0);
uint32_t region_id2 = merge.list[0].second;
assert_lt(region_id2, regions_similar.size());
const RegionSimilar& sim_region = regions_similar[region_id2];
if(sim_region.bw_length + sim_region.fw_length >= min_sim_length) {
output_merge = true;
}
}
if(output_merge) {
cout << endl << ":" << endl;
for(size_t k = 0; k < merge.list.size(); k++) {
uint32_t region_id1 = merge.list[k].first;
uint32_t region_id2 = merge.list[k].second;
assert_lt(region_id1, regions.size());
const Region& region = regions[region_id1];
assert_lt(region_id2, regions_similar.size());
const RegionSimilar& sim_region = regions_similar[region_id2];
cout << "\t";
cout << k << ") at " << region.pos << "\t" << region.fw_length << " bps\t"
<< (sim_region.fw ? "+" : "-") << "\tat " << sim_region.pos << "\t-" << sim_region.bw_length << "\t+" << sim_region.fw_length << endl;
}
cout << endl << endl;
}
#endif
assert_gt(merge.list.size(), 0);
for(size_t k = 0; k < merge.list.size(); k++) {
uint32_t region_id1 = merge.list[k].first;
assert_lt(region_id1, regions.size());
Region& region1 = regions[region_id1];
uint32_t cmp_region_id1 = merge.list[k].second;
assert_lt(cmp_region_id1, regions_similar.size());
const RegionSimilar& cmp_region1 = regions_similar[cmp_region_id1];
if(cmp_region1.fw) {
region1.fw_length = cmp_region1.fw_length;
region1.bw_length = cmp_region1.bw_length;
} else {
region1.fw_length = cmp_region1.fw_length > 0 ? cmp_region1.bw_length + 1 : 0;
region1.bw_length = cmp_region1.fw_length > 0 ? cmp_region1.fw_length - 1 : 0;
}
}