997 lines
36 KiB
C++
997 lines
36 KiB
C++
/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 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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* HISAT 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <iostream>
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#include <fstream>
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#include <string>
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#include <cassert>
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#include <getopt.h>
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#include <algorithm>
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#include "assert_helpers.h"
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#include "endian_swap.h"
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#include "formats.h"
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#include "sequence_io.h"
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#include "tokenize.h"
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#include "timer.h"
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#include "ref_read.h"
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#include "filebuf.h"
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#include "reference.h"
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#include "ds.h"
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#include "gfm.h"
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#include "aligner_sw.h"
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#include "aligner_result.h"
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#include "search_globals.h"
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#include "scoring.h"
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#include "mask.h"
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#include "repeat_builder.h"
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#include "utility_3n.h"
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/**
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* \file Driver for the bowtie-build indexing tool.
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*/
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#include <algorithm>
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#include <cstdlib>
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#include <fstream>
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#include <iostream>
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#include <vector>
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MemoryTally gMemTally;
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// Build parameters
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int verbose;
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static int sanityCheck;
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static int format;
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static TIndexOffU bmax;
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static TIndexOffU bmaxMultSqrt;
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static uint32_t bmaxDivN;
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static int dcv;
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static int noDc;
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static int entireSA;
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static int seed;
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static int showVersion;
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// GFM parameters
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static int32_t lineRate;
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static bool lineRate_provided;
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static int32_t linesPerSide;
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static int32_t offRate;
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static int32_t ftabChars;
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static int32_t localOffRate;
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static int32_t localFtabChars;
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static int bigEndian;
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static bool autoMem;
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static int nthreads; // number of pthreads operating concurrently
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static string wrapper;
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static TIndexOffU seed_length;
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static TIndexOffU seed_count;
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static TIndexOffU repeat_count;
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static TIndexOffU min_repeat_length;
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static TIndexOffU max_repeat_length;
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static EList<pair<TIndexOffU, TIndexOffU> > repeat_length_pair;
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static TIndexOffU max_repeat_edit;
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static TIndexOffU max_repeat_matchlen;
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static bool symmetric_extend;
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static bool repeat_indel;
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static bool forward_only;
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static bool CGtoTG;
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static string repeat_str1;
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static string repeat_str2;
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TIndexOffU max_seed_mm;
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TIndexOffU max_seed_repeat;
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TIndexOffU max_seed_extlen;
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static bool save_sa;
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static bool load_sa;
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bool threeN = false;
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char convertedFrom;
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char convertedTo;
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char convertedFromComplement;
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char convertedToComplement;
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bool base_change_entered;
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static void resetOptions() {
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verbose = true; // be talkative (default)
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sanityCheck = 0; // do slow sanity checks
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format = FASTA; // input sequence format
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bmax = OFF_MASK; // max blockwise SA bucket size
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bmaxMultSqrt = OFF_MASK; // same, as multplier of sqrt(n)
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bmaxDivN = 4; // same, as divisor of n
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dcv = 1024; // bwise SA difference-cover sample sz
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noDc = 0; // disable difference-cover sample
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entireSA = 0; // 1 = disable blockwise SA
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seed = 0; // srandom seed
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showVersion = 0; // just print version and quit?
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// GFM parameters
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lineRate = GFM<TIndexOffU>::default_lineRate_gfm;
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lineRate_provided = false;
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linesPerSide = 1; // 1 64-byte line on a side
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offRate = 4; // sample 1 out of 16 SA elts
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ftabChars = 10; // 10 chars in initial lookup table
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localOffRate = 3;
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localFtabChars = 6;
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bigEndian = 0; // little endian
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autoMem = true; // automatically adjust memory usage parameters
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nthreads = 1;
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seed_length = 50;
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seed_count = 5;
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min_repeat_length = 100;
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max_repeat_length = numeric_limits<uint16_t>::max();
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repeat_length_pair.clear();
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repeat_count = 5;
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max_repeat_edit = 10;
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max_repeat_matchlen = min_repeat_length / 2; // half of repeat_length
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repeat_indel = false;
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symmetric_extend = true;
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forward_only = false;
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CGtoTG = false;
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max_seed_mm = 5;
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max_seed_repeat = 5;
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max_seed_extlen = 25;
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save_sa = false;
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load_sa = false;
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wrapper.clear();
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threeN = false;
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convertedFrom = 'C';
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convertedTo = 'T';
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convertedFromComplement = asc2dnacomp[convertedFrom];
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convertedToComplement = asc2dnacomp[convertedTo];
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base_change_entered = false;
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}
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// Argument constants for getopts
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enum {
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ARG_BMAX = 256,
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ARG_BMAX_MULT,
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ARG_BMAX_DIV,
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ARG_DCV,
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ARG_SEED,
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ARG_CUTOFF,
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ARG_PMAP,
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ARG_NTOA,
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ARG_USAGE,
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ARG_REVERSE_EACH,
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ARG_SA,
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ARG_SEED_LENGTH,
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ARG_SEED_COUNT,
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ARG_MIN_REPEAT_LENGTH,
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ARG_MAX_REPEAT_LENGTH,
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ARG_REPEAT_LENGTH,
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ARG_REPEAT_COUNT,
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ARG_REPEAT_EDIT,
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ARG_REPEAT_MATCHLEN,
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ARG_REPEAT_INDEL,
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ARG_WRAPPER,
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ARG_ASYMMETRIC_EXTEND,
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ARG_FORWARD_ONLY,
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ARG_CGTOTG,
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ARG_REPEAT_STR1,
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ARG_REPEAT_STR2,
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ARG_MAX_SEED_MM,
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ARG_MAX_SEED_REPEAT,
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ARG_MAX_SEED_EXTLEN,
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ARG_SAVE_SA,
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ARG_LOAD_SA,
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ARG_3N,
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ARG_BASE_CHANGE
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};
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/**
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* Print a detailed usage message to the provided output stream.
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*/
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static void printUsage(ostream& out) {
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out << "HISAT2 version " << string(HISAT2_VERSION).c_str() << " by Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>" << endl;
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string tool_name = "hisat2-repeat";
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out << "Usage: " << tool_name << " [options]* <reference_in>" << endl
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<< " reference_in comma-separated list of files with ref sequences" << endl
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<< "Options:" << endl
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<< " -c reference sequences given on cmd line (as" << endl
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<< " <reference_in>)" << endl;
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if(wrapper == "basic-0") {
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out << " --large-index force generated index to be 'large', even if ref" << endl
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<< " has fewer than 4 billion nucleotides" << endl;
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}
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out << " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting" << endl
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<< " -p <int> number of threads" << endl
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<< " --bmax <int> max bucket sz for blockwise suffix-array builder" << endl
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<< " --bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)" << endl
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<< " --dcv <int> diff-cover period for blockwise (default: 1024)" << endl
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<< " --nodc disable diff-cover (algorithm becomes quadratic)" << endl
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<< " --seed-length <int> seed length (default: 50)" << endl
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<< " --seed-count <int> seed count (default: 5)" << endl
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<< " --min-repeat-length <int> minimum repeat length (default: 100)" << endl
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<< " --max-repeat-length <int> maximum repeat length (default: 65535)" << endl
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<< " --repeat-length <int>-<int>[,<int>-<int>] minimum-maximum repeat length pairs" << endl
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<< " --repeat-count <int> minimum repeat count (default: 5)" << endl
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<< " --repeat-edit <int> maximum repeat edit distance (default: 10)" << endl
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<< " --repeat-matchlen <int>" << endl
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<< " --repeat-indel" << endl
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<< " --repeat-str1" << endl
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<< " --repeat-str2" << endl
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<< " --asymmetric-extend extend seeds asymmetrically" << endl
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<< " --forward-only use forward strand only" << endl
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<< " --CGtoTG change CG to TG" << endl
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<< " --max-seed-mm <int>" << endl
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<< " --max-seed-repeat <int>" << endl
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<< " --max-seed-extlen <int>" << endl
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<< " --save-sa" << endl
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<< " --load-sa" << endl
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<< " --3N make 3N repeat database" << endl
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<< " --base-change <chr,chr> the converted nucleotide and converted to nucleotide (default:C,T)" << endl
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<< " -q/--quiet disable verbose output (for debugging)" << endl
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<< " -h/--help print detailed description of tool and its options" << endl
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<< " --usage print this usage message" << endl
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<< " --version print version information and quit" << endl
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;
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}
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static const char *short_options = "qrap:h?nscfl:i:o:t:h:3C";
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static struct option long_options[] = {
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{(char*)"quiet", no_argument, 0, 'q'},
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{(char*)"sanity", no_argument, 0, 's'},
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{(char*)"threads", required_argument, 0, 'p'},
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{(char*)"little", no_argument, &bigEndian, 0},
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{(char*)"big", no_argument, &bigEndian, 1},
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{(char*)"bmax", required_argument, 0, ARG_BMAX},
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{(char*)"bmaxmultsqrt", required_argument, 0, ARG_BMAX_MULT},
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{(char*)"bmaxdivn", required_argument, 0, ARG_BMAX_DIV},
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{(char*)"dcv", required_argument, 0, ARG_DCV},
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{(char*)"nodc", no_argument, &noDc, 1},
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{(char*)"seed", required_argument, 0, ARG_SEED},
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{(char*)"entiresa", no_argument, &entireSA, 1},
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{(char*)"version", no_argument, &showVersion, 1},
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{(char*)"noauto", no_argument, 0, 'a'},
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{(char*)"noblocks", required_argument, 0, 'n'},
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{(char*)"linerate", required_argument, 0, 'l'},
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{(char*)"linesperside", required_argument, 0, 'i'},
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{(char*)"usage", no_argument, 0, ARG_USAGE},
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{(char*)"seed-length", required_argument, 0, ARG_SEED_LENGTH},
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{(char*)"seed-count", required_argument, 0, ARG_SEED_COUNT},
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{(char*)"min-repeat-length", required_argument, 0, ARG_MIN_REPEAT_LENGTH},
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{(char*)"max-repeat-length", required_argument, 0, ARG_MAX_REPEAT_LENGTH},
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{(char*)"repeat-length", required_argument, 0, ARG_REPEAT_LENGTH},
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{(char*)"repeat-count", required_argument, 0, ARG_REPEAT_COUNT},
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{(char*)"repeat-edit", required_argument, 0, ARG_REPEAT_EDIT},
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{(char*)"repeat-matchlen",required_argument, 0, ARG_REPEAT_MATCHLEN},
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{(char*)"repeat-indel", no_argument, 0, ARG_REPEAT_INDEL},
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{(char*)"wrapper", required_argument, 0, ARG_WRAPPER},
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{(char*)"asymmetric-extend", no_argument, 0, ARG_ASYMMETRIC_EXTEND},
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{(char*)"forward-only", no_argument, 0, ARG_FORWARD_ONLY},
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{(char*)"CGtoTG", no_argument, 0, ARG_CGTOTG},
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{(char*)"repeat-str1", required_argument, 0, ARG_REPEAT_STR1},
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{(char*)"repeat-str2", required_argument, 0, ARG_REPEAT_STR2},
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{(char*)"max-seed-mm", required_argument, 0, ARG_MAX_SEED_MM},
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{(char*)"max-seed-repeat",required_argument, 0, ARG_MAX_SEED_REPEAT},
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{(char*)"max-seed-extlen",required_argument, 0, ARG_MAX_SEED_EXTLEN},
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{(char*)"save-sa", no_argument, 0, ARG_SAVE_SA},
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{(char*)"load-sa", no_argument, 0, ARG_LOAD_SA},
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{(char*)"3N", no_argument, 0, ARG_3N},
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{(char*)"base-change", required_argument, 0, ARG_BASE_CHANGE},
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{(char*)0, 0, 0, 0} // terminator
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};
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/**
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* Parse an int out of optarg and enforce that it be at least 'lower';
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* if it is less than 'lower', then output the given error message and
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* exit with an error and a usage message.
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*/
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template<typename T>
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static T parseNumber(const char *str, T lower, const char *errmsg)
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{
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char *endPtr= NULL;
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T t = (T)strtoll(str, &endPtr, 10);
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if(endPtr != NULL) {
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if(t < lower) {
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cerr << errmsg << endl;
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printUsage(cerr);
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throw 1;
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}
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return t;
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}
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cerr << errmsg << endl;
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printUsage(cerr);
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throw 1;
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return -1;
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}
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template<typename T>
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static T parseNumber(T lower, const char *errmsg) {
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return parseNumber(optarg, lower, errmsg);
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}
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static void parsePair(EList<pair<TIndexOffU, TIndexOffU> >& repeat_pair)
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{
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string tok;
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istringstream ss(optarg);
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while(getline(ss, tok, ',')) {
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if(tok.empty()) {
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continue;
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}
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TIndexOffU min_len, max_len;
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size_t pos = tok.find('-');
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if(pos == string::npos) {
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// min
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min_len = parseNumber<TIndexOffU>(tok.c_str(), 1, "min-repeat-length must be at least 1");
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max_len = numeric_limits<uint16_t>::max();
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} else if(pos == tok.length() - 1) {
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// min-
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min_len = parseNumber<TIndexOffU>(tok.substr(0, pos).c_str(), 1, "min-repeat-length must be at least 1");
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max_len = numeric_limits<uint16_t>::max();
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} else if(pos == 0) {
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// -max
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// not support?
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min_len = 100;
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max_len = parseNumber<TIndexOffU>(tok.substr(pos + 1).c_str(), 1, "max-repeat-length must be at least 1");
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} else {
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min_len = parseNumber<TIndexOffU>(tok.substr(0, pos).c_str(), 1, "min-repeat-length must be at least 1");
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max_len = parseNumber<TIndexOffU>(tok.substr(pos + 1).c_str(), 1, "max-repeat-length must be at least 1");
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}
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if(min_len > max_len) {
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printUsage(cerr);
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throw 1;
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}
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if(max_len > numeric_limits<uint16_t>::max()) {
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printUsage(cerr);
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throw 1;
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}
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repeat_pair.push_back(pair<TIndexOffU, TIndexOffU>(min_len, max_len));
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}
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}
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/**
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* Read command-line arguments
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*/
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static void parseOptions(int argc, const char **argv) {
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int option_index = 0;
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int next_option;
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bool saw_max_repeat_matchlen = false;
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do {
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next_option = getopt_long(
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argc, const_cast<char**>(argv),
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short_options, long_options, &option_index);
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switch (next_option) {
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case ARG_WRAPPER:
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wrapper = optarg;
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break;
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case 'f': format = FASTA; break;
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case 'c': format = CMDLINE; break;
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//case 'p': packed = true; break;
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case 'C':
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cerr << "Error: -C specified but Bowtie 2 does not support colorspace input." << endl;
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throw 1;
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break;
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case 'l':
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lineRate = parseNumber<int>(3, "-l/--lineRate arg must be at least 3");
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lineRate_provided = true;
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break;
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case 'i':
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linesPerSide = parseNumber<int>(1, "-i/--linesPerSide arg must be at least 1");
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break;
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case 'o':
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offRate = parseNumber<int>(0, "-o/--offRate arg must be at least 0");
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break;
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case 'n':
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// all f-s is used to mean "not set", so put 'e' on end
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bmax = 0xfffffffe;
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break;
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case 'h':
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case ARG_USAGE:
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printUsage(cout);
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throw 0;
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break;
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case ARG_BMAX:
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bmax = parseNumber<TIndexOffU>(1, "--bmax arg must be at least 1");
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bmaxMultSqrt = OFF_MASK; // don't use multSqrt
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bmaxDivN = 0xffffffff; // don't use multSqrt
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break;
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case ARG_BMAX_MULT:
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bmaxMultSqrt = parseNumber<TIndexOffU>(1, "--bmaxmultsqrt arg must be at least 1");
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bmax = OFF_MASK; // don't use bmax
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bmaxDivN = 0xffffffff; // don't use multSqrt
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break;
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case ARG_BMAX_DIV:
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bmaxDivN = parseNumber<uint32_t>(1, "--bmaxdivn arg must be at least 1");
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bmax = OFF_MASK; // don't use bmax
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bmaxMultSqrt = OFF_MASK; // don't use multSqrt
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break;
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case ARG_DCV:
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dcv = parseNumber<int>(3, "--dcv arg must be at least 3");
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break;
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case ARG_SEED:
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seed = parseNumber<int>(0, "--seed arg must be at least 0");
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break;
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case ARG_SEED_LENGTH:
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seed_length = parseNumber<TIndexOffU>(1, "--seed-length arg must be at least 1");
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break;
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case ARG_SEED_COUNT:
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seed_count = parseNumber<TIndexOffU>(2, "--repeat-count arg must be at least 2");
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break;
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case ARG_MIN_REPEAT_LENGTH:
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min_repeat_length = parseNumber<TIndexOffU>(1, "--min-repeat-length arg must be at least 1");
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break;
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case ARG_MAX_REPEAT_LENGTH:
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max_repeat_length = parseNumber<TIndexOffU>(1, "--max-repeat-length arg must be at least 1");
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break;
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case ARG_REPEAT_LENGTH:
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parsePair(repeat_length_pair);
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break;
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case ARG_REPEAT_COUNT:
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repeat_count = parseNumber<TIndexOffU>(2, "--repeat-count arg must be at least 2");
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break;
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case ARG_REPEAT_EDIT:
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max_repeat_edit = parseNumber<TIndexOffU>(0, "--repeat-edit arg must be at least 0");
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break;
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case ARG_REPEAT_MATCHLEN:
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max_repeat_matchlen = parseNumber<TIndexOffU>(0, "--repeat-matchlen arg must be at least 0");
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saw_max_repeat_matchlen = true;
|
||
break;
|
||
case ARG_REPEAT_INDEL:
|
||
repeat_indel = true;
|
||
break;
|
||
case ARG_ASYMMETRIC_EXTEND:
|
||
symmetric_extend = false;
|
||
break;
|
||
case ARG_FORWARD_ONLY:
|
||
forward_only = true;
|
||
break;
|
||
case ARG_CGTOTG:
|
||
CGtoTG = true;
|
||
break;
|
||
case ARG_REPEAT_STR1:
|
||
repeat_str1 = optarg;
|
||
break;
|
||
case ARG_REPEAT_STR2:
|
||
repeat_str2 = optarg;
|
||
break;
|
||
case ARG_MAX_SEED_MM:
|
||
max_seed_mm = parseNumber<TIndexOffU>(1, "--max_seed_mm arg must be at least 1");
|
||
break;
|
||
case ARG_MAX_SEED_REPEAT:
|
||
max_seed_repeat = parseNumber<TIndexOffU>(5, "--max_seed_repeat arg must be at least 5");
|
||
break;
|
||
case ARG_MAX_SEED_EXTLEN:
|
||
max_seed_extlen = parseNumber<TIndexOffU>(0, "--max_seed_extlen arg must be at least 0");
|
||
break;
|
||
case ARG_SAVE_SA:
|
||
save_sa = true;
|
||
break;
|
||
case ARG_LOAD_SA:
|
||
load_sa = true;
|
||
break;
|
||
case ARG_3N: {
|
||
threeN = true;
|
||
break;
|
||
}
|
||
case ARG_BASE_CHANGE: {
|
||
EList<string> args;
|
||
tokenize(optarg, ",", args);
|
||
if(args.size() != 2) {
|
||
cerr << "Error: expected 2 comma-separated "
|
||
<< "arguments to --base-change option, got " << args.size() << endl;
|
||
throw 1;
|
||
}
|
||
getConversion(args[0][0], args[1][0], convertedFrom, convertedTo);
|
||
|
||
string s = "ACGT";
|
||
if ((s.find(convertedFrom) == std::string::npos) || (s.find(convertedTo) == std::string::npos)) {
|
||
cerr << "Please enter the nucleotide in 'ACGT' for --base-change option." << endl;
|
||
throw 1;
|
||
}
|
||
|
||
if (convertedFrom == convertedTo) {
|
||
cerr << "Please enter two different base for --base-change option. If you wish to build the repeat database without nucleotide conversion, please do not use --base-change and --3N options." << endl;
|
||
throw 1;
|
||
}
|
||
|
||
base_change_entered = true;
|
||
}
|
||
case 'a': autoMem = false; break;
|
||
case 'q': verbose = false; break;
|
||
case 's': sanityCheck = true; break;
|
||
case 'p':
|
||
nthreads = parseNumber<int>(1, "-p arg must be at least 1");
|
||
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;
|
||
}
|
||
|
||
if(!saw_max_repeat_matchlen) {
|
||
max_repeat_matchlen = min_repeat_length / 2;
|
||
}
|
||
}
|
||
|
||
extern void initializeCntLut();
|
||
extern void initializeCntBit();
|
||
|
||
|
||
ConvertMatrix3N baseChange;
|
||
/**
|
||
* Drive the index construction process and optionally sanity-check the
|
||
* result.
|
||
*/
|
||
template<typename TStr>
|
||
static void driver(
|
||
const string& infile,
|
||
EList<string>& infiles,
|
||
const string& outfile,
|
||
bool packed,
|
||
bool forward_only,
|
||
bool CGtoTG)
|
||
{
|
||
initializeCntLut();
|
||
initializeCntBit();
|
||
|
||
EList<FileBuf*> is(MISC_CAT);
|
||
bool bisulfite = false;
|
||
bool nsToAs = false;
|
||
RefReadInParams refparams(false, false /* reverse */, nsToAs, bisulfite);
|
||
assert_gt(infiles.size(), 0);
|
||
if(format == CMDLINE) {
|
||
// Adapt sequence strings to stringstreams open for input
|
||
stringstream *ss = new stringstream();
|
||
for(size_t i = 0; i < infiles.size(); i++) {
|
||
(*ss) << ">" << i << endl << infiles[i].c_str() << endl;
|
||
}
|
||
FileBuf *fb = new FileBuf(ss);
|
||
assert(fb != NULL);
|
||
assert(!fb->eof());
|
||
assert(fb->get() == '>');
|
||
ASSERT_ONLY(fb->reset());
|
||
assert(!fb->eof());
|
||
is.push_back(fb);
|
||
} else {
|
||
// Adapt sequence files to ifstreams
|
||
for(size_t i = 0; i < infiles.size(); i++) {
|
||
FILE *f = fopen(infiles[i].c_str(), "r");
|
||
if (f == NULL) {
|
||
cerr << "Error: could not open "<< infiles[i].c_str() << endl;
|
||
throw 1;
|
||
}
|
||
FileBuf *fb = new FileBuf(f);
|
||
assert(fb != NULL);
|
||
if(fb->peek() == -1 || fb->eof()) {
|
||
cerr << "Warning: Empty fasta file: '" << infile.c_str() << "'" << endl;
|
||
continue;
|
||
}
|
||
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;
|
||
EList<string> ref_names;
|
||
std::pair<size_t, size_t> sztot;
|
||
{
|
||
if(verbose) cerr << "Reading reference sizes" << endl;
|
||
Timer _t(cerr, " Time reading reference sizes: ", verbose);
|
||
sztot = BitPairReference::szsFromFasta(is, "", bigEndian, refparams, szs, sanityCheck, &ref_names);
|
||
}
|
||
|
||
assert_gt(sztot.first, 0);
|
||
assert_gt(sztot.second, 0);
|
||
assert_gt(szs.size(), 0);
|
||
|
||
// Compose text strings into single string
|
||
cerr << "Calculating joined length" << endl;
|
||
TIndexOffU jlen = 0;
|
||
for(unsigned int i = 0; i < szs.size(); i++) {
|
||
jlen += (TIndexOffU)szs[i].len;
|
||
}
|
||
// assert_geq(jlen, sztot);
|
||
cerr << " Joined length: " << jlen << endl;
|
||
TStr s;
|
||
{
|
||
bool both_strand = forward_only ? false : true;
|
||
cerr << "Reserving space for joined string" << endl;
|
||
cerr << "Joining reference sequences" << endl;
|
||
Timer timer(cerr, " Time to join reference sequences: ", verbose);
|
||
GFM<TIndexOffU>::join<TStr>(
|
||
is,
|
||
szs,
|
||
(TIndexOffU) sztot.first,
|
||
refparams,
|
||
seed,
|
||
s,
|
||
both_strand, // include reverse complemented sequence
|
||
CGtoTG); //Change CG to TG
|
||
}
|
||
|
||
TStr sOriginal;
|
||
if (threeN) {
|
||
baseChange.restoreNormal();
|
||
bool both_strand = forward_only ? false : true;
|
||
for (int i = 0; i < is.size(); i++) {
|
||
is[i]->reset();
|
||
}
|
||
GFM<TIndexOffU>::join<TStr>(
|
||
is,
|
||
szs,
|
||
(TIndexOffU) sztot.first,
|
||
refparams,
|
||
seed,
|
||
sOriginal,
|
||
both_strand, // include reverse complemented sequence
|
||
CGtoTG); //Change CG to TG
|
||
baseChange.restoreConversion();
|
||
|
||
long long int guessLen = s.length() / 2;
|
||
for (TIndexOffU i = 0; i < guessLen; i++) {
|
||
int nt = sOriginal[guessLen - i - 1];
|
||
assert_range(0, 3, nt);
|
||
s[guessLen + i] = dnacomp[nt];
|
||
}
|
||
} else {
|
||
sOriginal = s;
|
||
}
|
||
|
||
// Successfully obtained joined reference string
|
||
#ifndef NDEBUG
|
||
if(forward_only) {
|
||
assert_geq(s.length(), jlen);
|
||
} else {
|
||
assert_geq(s.length(), jlen << 1);
|
||
}
|
||
#endif
|
||
|
||
|
||
BitPackedArray suffix_array;
|
||
|
||
bool sa_file_exist = false;
|
||
string sa_fname = outfile + ".rep.sa";
|
||
if(load_sa) {
|
||
ifstream fp(sa_fname, std::ifstream::binary);
|
||
sa_file_exist = fp.is_open();
|
||
}
|
||
|
||
if(load_sa && sa_file_exist) {
|
||
cerr << "Load SA from " << sa_fname << endl;
|
||
suffix_array.readFile(sa_fname);
|
||
} else {
|
||
suffix_array.init(s.length() + 1);
|
||
|
||
if(bmax != (TIndexOffU) OFF_MASK) {
|
||
// VMSG_NL("bmax according to bmax setting: " << bmax);
|
||
} else if(bmaxDivN != (uint32_t) OFF_MASK) {
|
||
bmax = max<uint32_t>(jlen / (bmaxDivN * nthreads), 1);
|
||
// VMSG_NL("bmax according to bmaxDivN setting: " << bmax);
|
||
} else {
|
||
bmax = (uint32_t) sqrt(s.length());
|
||
// VMSG_NL("bmax defaulted to: " << bmax);
|
||
}
|
||
int iter = 0;
|
||
bool first = true;
|
||
bool passMemExc = false, sanity = false;
|
||
// Look for bmax/dcv parameters that work.
|
||
while(true) {
|
||
if(!first && bmax < 40 && passMemExc) {
|
||
cerr << "Could not find appropriate bmax/dcv settings for building this index." << endl;
|
||
cerr << "Please try indexing this reference 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;
|
||
}
|
||
if(dcv > 4096) dcv = 4096;
|
||
if((iter % 6) == 5 && dcv < 4096 && dcv != 0) {
|
||
dcv <<= 1; // double difference-cover period
|
||
} else {
|
||
bmax -= (bmax >> 2); // reduce by 25%
|
||
}
|
||
iter++;
|
||
|
||
suffix_array.reset();
|
||
|
||
try {
|
||
cerr << "Using parameters --bmax " << bmax << endl;
|
||
if(dcv == 0) {
|
||
cerr << " and *no difference cover*" << endl;
|
||
} else {
|
||
cerr << " --dcv " << dcv << endl;
|
||
}
|
||
{
|
||
cerr << " Doing ahead-of-time memory usage test" << endl;
|
||
// Make a quick-and-dirty attempt to force a bad_alloc iff
|
||
// we would have thrown one eventually as part of
|
||
// constructing the DifferenceCoverSample
|
||
dcv <<= 1;
|
||
TIndexOffU sz = (TIndexOffU) DifferenceCoverSample<TStr>::simulateAllocs(s, dcv >> 1);
|
||
if(nthreads > 1) sz *= (nthreads + 1);
|
||
AutoArray<uint8_t> tmp(sz, EBWT_CAT);
|
||
dcv >>= 1;
|
||
// Likewise with the KarkkainenBlockwiseSA
|
||
sz = (TIndexOffU) KarkkainenBlockwiseSA<TStr>::simulateAllocs(s, bmax);
|
||
AutoArray<uint8_t> tmp2(sz, EBWT_CAT);
|
||
// Grab another 20 MB out of caution
|
||
AutoArray<uint32_t> extra(20 * 1024 * 1024, EBWT_CAT);
|
||
// If we made it here without throwing bad_alloc, then we
|
||
// passed the memory-usage stress test
|
||
cerr << " Passed! Constructing with these parameters: --bmax " << bmax << " --dcv " << dcv
|
||
<< endl;
|
||
cerr << "" << endl;
|
||
}
|
||
cerr << "Constructing suffix-array element generator" << endl;
|
||
|
||
KarkkainenBlockwiseSA<TStr> bsa(s,
|
||
bmax,
|
||
nthreads,
|
||
dcv,
|
||
seed,
|
||
sanity,
|
||
passMemExc,
|
||
false /* verbose */,
|
||
outfile);
|
||
|
||
assert(bsa.suffixItrIsReset());
|
||
assert_eq(bsa.size(), s.length() + 1);
|
||
|
||
TIndexOffU count = 0;
|
||
|
||
while(count < s.length() + 1) {
|
||
TIndexOffU saElt = bsa.nextSuffix();
|
||
count++;
|
||
|
||
if(count && (count % 10000000 == 0)) {
|
||
cerr << "SA count " << count << endl;
|
||
}
|
||
|
||
if(saElt == s.length()) {
|
||
assert_eq(count, s.length() + 1);
|
||
break;
|
||
}
|
||
|
||
suffix_array.pushBack(saElt);
|
||
}
|
||
|
||
break;
|
||
|
||
} catch (bad_alloc &e) {
|
||
if(passMemExc) {
|
||
cerr << " Ran out of memory; automatically trying more memory-economical parameters." << endl;
|
||
} else {
|
||
cerr << "Out of memory while constructing suffix array. Please try using a smaller" << endl
|
||
<< "number of blocks by specifying a smaller --bmax or a larger --bmaxdivn" << endl;
|
||
throw 1;
|
||
}
|
||
}
|
||
first = false;
|
||
}
|
||
|
||
if(save_sa) {
|
||
suffix_array.writeFile(sa_fname);
|
||
}
|
||
}
|
||
|
||
cerr << "suffix_array: " << endl;
|
||
suffix_array.dump();
|
||
|
||
|
||
// Build Repeats
|
||
{
|
||
if(repeat_length_pair.empty()) {
|
||
repeat_length_pair.push_back(pair<TIndexOffU, TIndexOffU>(min_repeat_length, max_repeat_length));
|
||
}
|
||
|
||
RepeatParameter rp;
|
||
rp.seed_len = seed_length;
|
||
rp.seed_count = seed_count;
|
||
rp.seed_mm = max_seed_mm;
|
||
rp.max_edit = max_repeat_edit;
|
||
rp.symmetric_extend = symmetric_extend;
|
||
rp.extend_unit_len = max_seed_extlen;
|
||
for(size_t i = 0; i < repeat_length_pair.size(); i++) {
|
||
rp.min_repeat_len = repeat_length_pair[i].first;
|
||
rp.max_repeat_len = repeat_length_pair[i].second;
|
||
rp.repeat_count = repeat_count;
|
||
rp.append_result = (i != 0);
|
||
|
||
RepeatBuilder<TStr> repeatBuilder(s,
|
||
sOriginal,
|
||
szs,
|
||
ref_names,
|
||
forward_only,
|
||
outfile);
|
||
cerr << "RepeatBuilder: " << outfile << " " << rp.min_repeat_len << "-" << rp.max_repeat_len << endl;
|
||
|
||
{
|
||
Timer _t(cerr, " Time reading suffix array: ", verbose);
|
||
repeatBuilder.readSA(rp, suffix_array);
|
||
}
|
||
|
||
repeatBuilder.build(rp);
|
||
repeatBuilder.saveFile(rp);
|
||
}
|
||
}
|
||
}
|
||
|
||
static const char *argv0 = NULL;
|
||
|
||
extern "C" {
|
||
/**
|
||
* main function. Parses command-line arguments.
|
||
*/
|
||
int hisat2_repeat(int argc, const char **argv) {
|
||
string outfile;
|
||
try {
|
||
// Reset all global state, including getopt state
|
||
opterr = optind = 1;
|
||
resetOptions();
|
||
|
||
string infile;
|
||
EList<string> infiles(MISC_CAT);
|
||
|
||
parseOptions(argc, argv);
|
||
argv0 = argv[0];
|
||
if(showVersion) {
|
||
cout << argv0 << " version " << string(HISAT2_VERSION).c_str() << endl;
|
||
if(sizeof(void*) == 4) {
|
||
cout << "32-bit" << endl;
|
||
} else if(sizeof(void*) == 8) {
|
||
cout << "64-bit" << endl;
|
||
} else {
|
||
cout << "Neither 32- nor 64-bit: sizeof(void*) = " << sizeof(void*) << endl;
|
||
}
|
||
cout << "Built on " << BUILD_HOST << endl;
|
||
cout << BUILD_TIME << endl;
|
||
cout << "Compiler: " << COMPILER_VERSION << endl;
|
||
cout << "Options: " << COMPILER_OPTIONS << endl;
|
||
cout << "Sizeof {int, long, long long, void*, size_t, off_t}: {"
|
||
<< sizeof(int)
|
||
<< ", " << sizeof(long) << ", " << sizeof(long long)
|
||
<< ", " << sizeof(void *) << ", " << sizeof(size_t)
|
||
<< ", " << sizeof(off_t) << "}" << endl;
|
||
return 0;
|
||
}
|
||
|
||
if (!threeN && base_change_entered) {
|
||
cerr << "To build hisat-3n repeat database, please add argument --3N. To build the hisat2 repeat database, please remove the argument --base-change." << endl;
|
||
printUsage(cerr);
|
||
throw 1;
|
||
}
|
||
if (threeN) {
|
||
convertedFromComplement = asc2dnacomp[convertedFrom];
|
||
convertedToComplement = asc2dnacomp[convertedTo];
|
||
}
|
||
// Get input filename
|
||
if(optind >= argc) {
|
||
cerr << "No input sequence or sequence file specified!" << endl;
|
||
printUsage(cerr);
|
||
return 1;
|
||
}
|
||
infile = argv[optind++];
|
||
|
||
if(optind >= argc) {
|
||
cerr << "No output file specified!" << endl;
|
||
printUsage(cerr);
|
||
return 1;
|
||
}
|
||
outfile = argv[optind++];
|
||
|
||
tokenize(infile, ",", infiles);
|
||
if(infiles.size() < 1) {
|
||
cerr << "Tokenized input file list was empty!" << endl;
|
||
printUsage(cerr);
|
||
return 1;
|
||
}
|
||
|
||
// Optionally summarize
|
||
if(verbose) {
|
||
cerr << "Settings:" << endl;
|
||
// << " Output files: \"" << outfile.c_str() << ".*." << gfm_ext << "\"" << endl;
|
||
cerr << " Endianness: " << (bigEndian? "big":"little") << endl
|
||
<< " Actual local endianness: " << (currentlyBigEndian()? "big":"little") << endl
|
||
<< " Sanity checking: " << (sanityCheck? "enabled":"disabled") << endl;
|
||
#ifdef NDEBUG
|
||
cerr << " Assertions: disabled" << endl;
|
||
#else
|
||
cerr << " Assertions: enabled" << endl;
|
||
#endif
|
||
cerr << " Random seed: " << seed << endl;
|
||
cerr << " Sizeofs: void*:" << sizeof(void*) << ", int:" << sizeof(int) << ", long:" << sizeof(long) << ", size_t:" << sizeof(size_t) << endl;
|
||
cerr << "Input files DNA, " << file_format_names[format].c_str() << ":" << endl;
|
||
for(size_t i = 0; i < infiles.size(); i++) {
|
||
cerr << " " << infiles[i].c_str() << endl;
|
||
}
|
||
}
|
||
// Seed random number generator
|
||
srand(seed);
|
||
{
|
||
Timer timer(cerr, "Total time for call to driver() for forward index: ", verbose);
|
||
try {
|
||
int nloop = threeN ? 2 : 1; // if threeN == true, nloop = 2. else one loop
|
||
for (int i = 0; i < nloop; i++) {
|
||
string tag = "";
|
||
if (threeN) {
|
||
tag += ".3n.";
|
||
if (i == 0) {
|
||
tag += convertedFrom;
|
||
tag += convertedTo;
|
||
baseChange.convert(convertedFrom, convertedTo);
|
||
} else {
|
||
tag += convertedFromComplement;
|
||
tag += convertedToComplement;
|
||
baseChange.convert(convertedFromComplement, convertedToComplement);
|
||
}
|
||
|
||
string indexFilename = outfile + tag + ".rep.fa";
|
||
if (fileExist(indexFilename)) {
|
||
cerr << "*** Find repeat database for " << outfile + tag << "，skip this repeat database building process." << endl;
|
||
cerr << " To re-build your hisat-3n repeat database, please delete the old index manually before running hisat2-repeat or hisat-3n-build." << endl;
|
||
continue;
|
||
}
|
||
}
|
||
driver<SString<char> >(infile, infiles, outfile + tag, false, forward_only, CGtoTG);
|
||
}
|
||
|
||
} catch(bad_alloc& e) {
|
||
if(autoMem) {
|
||
cerr << "Switching to a packed string representation." << endl;
|
||
} else {
|
||
throw e;
|
||
}
|
||
}
|
||
}
|
||
return 0;
|
||
} catch(std::exception& e) {
|
||
cerr << "Error: Encountered exception: '" << e.what() << "'" << endl;
|
||
cerr << "Command: ";
|
||
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
|
||
cerr << endl;
|
||
return 1;
|
||
} catch(int e) {
|
||
if(e != 0) {
|
||
cerr << "Error: Encountered internal HISAT2 exception (#" << e << ")" << endl;
|
||
cerr << "Command: ";
|
||
for(int i = 0; i < argc; i++) cerr << argv[i] << " ";
|
||
cerr << endl;
|
||
}
|
||
return e;
|
||
}
|
||
}
|
||
}
|