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ebwt_search.cpp
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ebwt_search.cpp
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#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <string>
#include <algorithm>
#include <cassert>
#include <stdexcept>
#include <seqan/find.h>
#include <getopt.h>
#include <vector>
#include "alphabet.h"
#include "assert_helpers.h"
#include "endian_swap.h"
#include "ebwt.h"
#include "formats.h"
#include "sequence_io.h"
#include "tokenize.h"
#include "hit.h"
#include "pat.h"
#include "bitset.h"
#include "threading.h"
#include "range_cache.h"
#include "refmap.h"
#include "annot.h"
#include "aligner.h"
#include "aligner_0mm.h"
#include "aligner_1mm.h"
#include "aligner_23mm.h"
#include "aligner_seed_mm.h"
#include "aligner_metrics.h"
#include "sam.h"
#ifdef CHUD_PROFILING
#include <CHUD/CHUD.h>
#endif
using namespace std;
using namespace seqan;
static vector<string> mates1; // mated reads (first mate)
static vector<string> mates2; // mated reads (second mate)
static vector<string> mates12; // mated reads (1st/2nd interleaved in 1 file)
static string adjustedEbwtFileBase;
static bool verbose; // be talkative
static bool startVerbose; // be talkative at startup
bool quiet; // print nothing but the alignments
static int sanityCheck; // enable expensive sanity checks
static int format; // default read format is FASTQ
static string origString; // reference text, or filename(s)
static int seed; // srandom() seed
static int timing; // whether to report basic timing data
static bool allHits; // for multihits, report just one
static bool rangeMode; // report BWT ranges instead of ref locs
static int showVersion; // just print version and quit?
static int ipause; // pause before maching?
static uint32_t qUpto; // max # of queries to read
static int trim5; // amount to trim from 5' end
static int trim3; // amount to trim from 3' end
static int reportOpps; // whether to report # of other mappings
static int offRate; // keep default offRate
static int isaRate; // keep default isaRate
static int mismatches; // allow 0 mismatches by default
static char *patDumpfile; // filename to dump patterns to
static bool solexaQuals; // quality strings are solexa quals, not phred, and subtract 64 (not 33)
static bool phred64Quals; // quality chars are phred, but must subtract 64 (not 33)
static bool integerQuals; // quality strings are space-separated strings of integers, not ASCII
static int maqLike; // do maq-like searching
static int seedLen; // seed length (changed in Maq 0.6.4 from 24)
static int seedMms; // # mismatches allowed in seed (maq's -n)
static int qualThresh; // max qual-weighted hamming dist (maq's -e)
static int maxBtsBetter; // max # backtracks allowed in half-and-half mode
static int maxBts; // max # backtracks allowed in half-and-half mode
static int nthreads; // number of pthreads operating concurrently
static output_types outType; // style of output
static bool randReadsNoSync; // true -> generate reads from per-thread random source
static int numRandomReads; // # random reads (see Random*PatternSource in pat.h)
static int lenRandomReads; // len of random reads (see Random*PatternSource in pat.h)
static bool noRefNames; // true -> print reference indexes; not names
static string dumpAlBase; // basename of same-format files to dump aligned reads to
static string dumpUnalBase; // basename of same-format files to dump unaligned reads to
static string dumpMaxBase; // basename of same-format files to dump reads with more than -m valid alignments to
static uint32_t khits; // number of hits per read; >1 is much slower
static uint32_t mhits; // don't report any hits if there are > mhits
static bool better; // true -> guarantee alignments from best possible stratum
static bool strata; // true -> don't stop at stratum boundaries
static bool refOut; // if true, alignments go to per-ref files
static int partitionSz; // output a partitioning key in first field
static bool noMaqRound; // true -> don't round quals to nearest 10 like maq
static bool fileParallel; // separate threads read separate input files in parallel
static bool useShmem; // use shared memory to hold the index
static bool useMm; // use memory-mapped files to hold the index
static bool mmSweep; // sweep through memory-mapped files immediately after mapping
static bool stateful; // use stateful aligners
static uint32_t prefetchWidth; // number of reads to process in parallel w/ --stateful
static uint32_t minInsert; // minimum insert size (Maq = 0, SOAP = 400)
static uint32_t maxInsert; // maximum insert size (Maq = 250, SOAP = 600)
static bool mate1fw; // -1 mate aligns in fw orientation on fw strand
static bool mate2fw; // -2 mate aligns in rc orientation on fw strand
static bool mateFwSet; // true -> user set --ff/--fr/--rf
static uint32_t mixedThresh; // threshold for when to switch to paired-end mixed mode (see aligner.h)
static uint32_t mixedAttemptLim; // number of attempts to make in "mixed mode" before giving up on orientation
static bool dontReconcileMates; // suppress pairwise all-versus-all way of resolving mates
static uint32_t cacheLimit; // ranges w/ size > limit will be cached
static uint32_t cacheSize; // # words per range cache
static int offBase; // offsets are 0-based by default, but configurable
static bool tryHard; // set very high maxBts, mixedAttemptLim
static uint32_t skipReads; // # reads/read pairs to skip
static bool nofw; // don't align fw orientation of read
static bool norc; // don't align rc orientation of read
static bool strandFix; // attempt to fix strand bias
static bool randomizeQuals; // randomize quality values
static bool stats; // print performance stats
static int chunkPoolMegabytes; // max MB to dedicate to best-first search frames per thread
static int chunkSz; // size of single chunk disbursed by ChunkPool
static bool chunkVerbose; // have chunk allocator output status messages?
static bool recal;
static int recalMaxCycle;
static int recalMaxQual;
static int recalQualShift;
static bool useV1;
static bool reportSe;
static const char * refMapFile; // file containing a map from index coordinates to another coordinate system
static const char * annotMapFile; // file containing a map from reference coordinates to annotations
static size_t fastaContLen;
static size_t fastaContFreq;
static bool hadoopOut; // print Hadoop status and summary messages
static bool fuzzy;
static bool fullRef;
static bool samNoQnameTrunc; // don't truncate QNAME field at first whitespace
static bool samNoHead; // don't print any header lines in SAM output
static bool samNoSQ; // don't print @SQ header lines
bool color; // true -> inputs are colorspace
bool colorExEnds; // true -> nucleotides on either end of decoded cspace alignment should be excluded
static string rgs; // SAM outputs for @RG header line
int snpPhred; // probability of SNP, for scoring colorspace alignments
static Bitset suppressOuts(64); // output fields to suppress
static bool sampleMax; // whether to report a random alignment when maxed-out via -m/-M
static int defaultMapq; // default mapping quality to print in SAM mode
bool colorSeq; // true -> show colorspace alignments as colors, not decoded bases
bool colorQual; // true -> show colorspace qualities as original quals, not decoded quals
static bool printCost; // true -> print stratum and cost
bool showSeed;
static vector<string> qualities;
static vector<string> qualities1;
static vector<string> qualities2;
static string wrapper; // Type of wrapper script
bool gAllowMateContainment;
bool gReportColorPrimer;
MUTEX_T gLock;
static void resetOptions() {
mates1.clear();
mates2.clear();
mates12.clear();
adjustedEbwtFileBase = "";
verbose = 0;
startVerbose = 0;
quiet = false;
sanityCheck = 0; // enable expensive sanity checks
format = FASTQ; // default read format is FASTQ
origString = ""; // reference text, or filename(s)
seed = 0; // srandom() seed
timing = 0; // whether to report basic timing data
allHits = false; // for multihits, report just one
rangeMode = false; // report BWT ranges instead of ref locs
showVersion = 0; // just print version and quit?
ipause = 0; // pause before maching?
qUpto = 0xffffffff; // max # of queries to read
trim5 = 0; // amount to trim from 5' end
trim3 = 0; // amount to trim from 3' end
reportOpps = 0; // whether to report # of other mappings
offRate = -1; // keep default offRate
isaRate = -1; // keep default isaRate
mismatches = 0; // allow 0 mismatches by default
patDumpfile = NULL; // filename to dump patterns to
solexaQuals = false; // quality strings are solexa quals, not phred, and subtract 64 (not 33)
phred64Quals = false; // quality chars are phred, but must subtract 64 (not 33)
integerQuals = false; // quality strings are space-separated strings of integers, not ASCII
maqLike = 1; // do maq-like searching
seedLen = 28; // seed length (changed in Maq 0.6.4 from 24)
seedMms = 2; // # mismatches allowed in seed (maq's -n)
qualThresh = 70; // max qual-weighted hamming dist (maq's -e)
maxBtsBetter = 125; // max # backtracks allowed in half-and-half mode
maxBts = 800; // max # backtracks allowed in half-and-half mode
nthreads = 1; // number of pthreads operating concurrently
outType = OUTPUT_FULL; // style of output
randReadsNoSync = false; // true -> generate reads from per-thread random source
numRandomReads = 50000000; // # random reads (see Random*PatternSource in pat.h)
lenRandomReads = 35; // len of random reads (see Random*PatternSource in pat.h)
noRefNames = false; // true -> print reference indexes; not names
dumpAlBase = ""; // basename of same-format files to dump aligned reads to
dumpUnalBase = ""; // basename of same-format files to dump unaligned reads to
dumpMaxBase = ""; // basename of same-format files to dump reads with more than -m valid alignments to
khits = 1; // number of hits per read; >1 is much slower
mhits = 0xffffffff; // don't report any hits if there are > mhits
better = false; // true -> guarantee alignments from best possible stratum
strata = false; // true -> don't stop at stratum boundaries
refOut = false; // if true, alignments go to per-ref files
partitionSz = 0; // output a partitioning key in first field
noMaqRound = false; // true -> don't round quals to nearest 10 like maq
fileParallel = false; // separate threads read separate input files in parallel
useShmem = false; // use shared memory to hold the index
useMm = false; // use memory-mapped files to hold the index
mmSweep = false; // sweep through memory-mapped files immediately after mapping
stateful = false; // use stateful aligners
prefetchWidth = 1; // number of reads to process in parallel w/ --stateful
minInsert = 0; // minimum insert size (Maq = 0, SOAP = 400)
maxInsert = 250; // maximum insert size (Maq = 250, SOAP = 600)
mate1fw = true; // -1 mate aligns in fw orientation on fw strand
mate2fw = false; // -2 mate aligns in rc orientation on fw strand
mateFwSet = false; // true -> user set mate1fw/mate2fw with --ff/--fr/--rf
mixedThresh = 4; // threshold for when to switch to paired-end mixed mode (see aligner.h)
mixedAttemptLim = 100; // number of attempts to make in "mixed mode" before giving up on orientation
dontReconcileMates = true; // suppress pairwise all-versus-all way of resolving mates
cacheLimit = 5; // ranges w/ size > limit will be cached
cacheSize = 0; // # words per range cache
offBase = 0; // offsets are 0-based by default, but configurable
tryHard = false; // set very high maxBts, mixedAttemptLim
skipReads = 0; // # reads/read pairs to skip
nofw = false; // don't align fw orientation of read
norc = false; // don't align rc orientation of read
strandFix = true; // attempt to fix strand bias
randomizeQuals = false; // randomize quality values
stats = false; // print performance stats
chunkPoolMegabytes = 64; // max MB to dedicate to best-first search frames per thread
chunkSz = 256; // size of single chunk disbursed by ChunkPool (in KB)
chunkVerbose = false; // have chunk allocator output status messages?
recal = false;
recalMaxCycle = 64;
recalMaxQual = 40;
recalQualShift = 2;
useV1 = true;
reportSe = false;
refMapFile = NULL; // file containing a map from index coordinates to another coordinate system
annotMapFile = NULL; // file containing a map from reference coordinates to annotations
fastaContLen = 0;
fastaContFreq = 0;
hadoopOut = false; // print Hadoop status and summary messages
fuzzy = false; // reads will have alternate basecalls w/ qualities
fullRef = false; // print entire reference name instead of just up to 1st space
samNoQnameTrunc = false; // don't truncate at first whitespace?
samNoHead = false; // don't print any header lines in SAM output
samNoSQ = false; // don't print @SQ header lines
color = false; // don't align in colorspace by default
colorExEnds = true; // true -> nucleotides on either end of decoded cspace alignment should be excluded
rgs = ""; // SAM outputs for @RG header line
snpPhred = 30; // probability of SNP, for scoring colorspace alignments
suppressOuts.clear(); // output fields to suppress
sampleMax = false;
defaultMapq = 255;
colorSeq = false; // true -> show colorspace alignments as colors, not decoded bases
colorQual = false; // true -> show colorspace qualities as original quals, not decoded quals
printCost = false; // true -> print cost and stratum
showSeed = false; // true -> print per-read pseudo-random seed
qualities.clear();
qualities1.clear();
qualities2.clear();
wrapper.clear();
gAllowMateContainment = false; // true -> alignments where one mate lies inside the other are valid
gReportColorPrimer = false; // true -> print flag with trimmed color primer and downstream color
}
// mating constraints
static const char *short_options = "fF:qbzhcu:rv:s:at3:5:o:e:n:l:w:p:k:m:M:1:2:I:X:x:B:ySCQ:";
enum {
ARG_ORIG = 256,
ARG_SEED,
ARG_DUMP_PATS,
ARG_RANGE,
ARG_CONCISE,
ARG_SOLEXA_QUALS,
ARG_MAXBTS,
ARG_VERBOSE,
ARG_STARTVERBOSE,
ARG_QUIET,
ARG_RANDOM_READS,
ARG_RANDOM_READS_NOSYNC,
ARG_NOOUT,
ARG_FAST,
ARG_AL,
ARG_UN,
ARG_MAXDUMP,
ARG_REFIDX,
ARG_SANITY,
ARG_OLDBEST,
ARG_BETTER,
ARG_BEST,
ARG_REFOUT,
ARG_ISARATE,
ARG_PARTITION,
ARG_integerQuals,
ARG_NOMAQROUND,
ARG_FILEPAR,
ARG_SHMEM,
ARG_MM,
ARG_MMSWEEP,
ARG_STATEFUL,
ARG_PREFETCH_WIDTH,
ARG_FF,
ARG_FR,
ARG_RF,
ARG_MIXED_ATTEMPTS,
ARG_NO_RECONCILE,
ARG_CACHE_LIM,
ARG_CACHE_SZ,
ARG_NO_FW,
ARG_NO_RC,
ARG_SKIP,
ARG_STRAND_FIX,
ARG_RANDOMIZE_QUALS,
ARG_STATS,
ARG_ONETWO,
ARG_PHRED64,
ARG_PHRED33,
ARG_CHUNKMBS,
ARG_CHUNKSZ,
ARG_CHUNKVERBOSE,
ARG_RECAL,
ARG_STRATA,
ARG_PEV2,
ARG_REFMAP,
ARG_ANNOTMAP,
ARG_REPORTSE,
ARG_HADOOPOUT,
ARG_FUZZY,
ARG_FULLREF,
ARG_USAGE,
ARG_SNPPHRED,
ARG_SNPFRAC,
ARG_SAM_NO_QNAME_TRUNC,
ARG_SAM_NOHEAD,
ARG_SAM_NOSQ,
ARG_SAM_RG,
ARG_SUPPRESS_FIELDS,
ARG_DEFAULT_MAPQ,
ARG_COLOR_SEQ,
ARG_COLOR_QUAL,
ARG_COST,
ARG_COLOR_KEEP_ENDS,
ARG_SHOWSEED,
ARG_QUALS1,
ARG_QUALS2,
ARG_ALLOW_CONTAIN,
ARG_COLOR_PRIMER,
ARG_WRAPPER
};
static struct option long_options[] = {
{(char*)"verbose", no_argument, 0, ARG_VERBOSE},
{(char*)"startverbose", no_argument, 0, ARG_STARTVERBOSE},
{(char*)"quiet", no_argument, 0, ARG_QUIET},
{(char*)"sanity", no_argument, 0, ARG_SANITY},
{(char*)"pause", no_argument, &ipause, 1},
{(char*)"orig", required_argument, 0, ARG_ORIG},
{(char*)"all", no_argument, 0, 'a'},
{(char*)"concise", no_argument, 0, ARG_CONCISE},
{(char*)"noout", no_argument, 0, ARG_NOOUT},
{(char*)"solexa-quals", no_argument, 0, ARG_SOLEXA_QUALS},
{(char*)"integer-quals",no_argument, 0, ARG_integerQuals},
{(char*)"time", no_argument, 0, 't'},
{(char*)"trim3", required_argument, 0, '3'},
{(char*)"trim5", required_argument, 0, '5'},
{(char*)"seed", required_argument, 0, ARG_SEED},
{(char*)"qupto", required_argument, 0, 'u'},
{(char*)"al", required_argument, 0, ARG_AL},
{(char*)"un", required_argument, 0, ARG_UN},
{(char*)"max", required_argument, 0, ARG_MAXDUMP},
{(char*)"offrate", required_argument, 0, 'o'},
{(char*)"isarate", required_argument, 0, ARG_ISARATE},
{(char*)"reportopps", no_argument, &reportOpps, 1},
{(char*)"version", no_argument, &showVersion, 1},
{(char*)"dumppats", required_argument, 0, ARG_DUMP_PATS},
{(char*)"maqerr", required_argument, 0, 'e'},
{(char*)"seedlen", required_argument, 0, 'l'},
{(char*)"seedmms", required_argument, 0, 'n'},
{(char*)"filepar", no_argument, 0, ARG_FILEPAR},
{(char*)"help", no_argument, 0, 'h'},
{(char*)"threads", required_argument, 0, 'p'},
{(char*)"khits", required_argument, 0, 'k'},
{(char*)"mhits", required_argument, 0, 'm'},
{(char*)"minins", required_argument, 0, 'I'},
{(char*)"maxins", required_argument, 0, 'X'},
{(char*)"quals", required_argument, 0, 'Q'},
{(char*)"Q1", required_argument, 0, ARG_QUALS1},
{(char*)"Q2", required_argument, 0, ARG_QUALS2},
{(char*)"best", no_argument, 0, ARG_BEST},
{(char*)"better", no_argument, 0, ARG_BETTER},
{(char*)"oldbest", no_argument, 0, ARG_OLDBEST},
{(char*)"strata", no_argument, 0, ARG_STRATA},
{(char*)"nomaqround", no_argument, 0, ARG_NOMAQROUND},
{(char*)"refidx", no_argument, 0, ARG_REFIDX},
{(char*)"range", no_argument, 0, ARG_RANGE},
{(char*)"maxbts", required_argument, 0, ARG_MAXBTS},
{(char*)"randread", no_argument, 0, ARG_RANDOM_READS},
{(char*)"randreadnosync", no_argument, 0, ARG_RANDOM_READS_NOSYNC},
{(char*)"phased", no_argument, 0, 'z'},
{(char*)"refout", no_argument, 0, ARG_REFOUT},
{(char*)"partition", required_argument, 0, ARG_PARTITION},
{(char*)"stateful", no_argument, 0, ARG_STATEFUL},
{(char*)"prewidth", required_argument, 0, ARG_PREFETCH_WIDTH},
{(char*)"ff", no_argument, 0, ARG_FF},
{(char*)"fr", no_argument, 0, ARG_FR},
{(char*)"rf", no_argument, 0, ARG_RF},
{(char*)"mixthresh", required_argument, 0, 'x'},
{(char*)"pairtries", required_argument, 0, ARG_MIXED_ATTEMPTS},
{(char*)"noreconcile", no_argument, 0, ARG_NO_RECONCILE},
{(char*)"cachelim", required_argument, 0, ARG_CACHE_LIM},
{(char*)"cachesz", required_argument, 0, ARG_CACHE_SZ},
{(char*)"nofw", no_argument, 0, ARG_NO_FW},
{(char*)"norc", no_argument, 0, ARG_NO_RC},
{(char*)"offbase", required_argument, 0, 'B'},
{(char*)"tryhard", no_argument, 0, 'y'},
{(char*)"skip", required_argument, 0, 's'},
{(char*)"strandfix", no_argument, 0, ARG_STRAND_FIX},
{(char*)"randquals", no_argument, 0, ARG_RANDOMIZE_QUALS},
{(char*)"stats", no_argument, 0, ARG_STATS},
{(char*)"12", required_argument, 0, ARG_ONETWO},
{(char*)"phred33-quals", no_argument, 0, ARG_PHRED33},
{(char*)"phred64-quals", no_argument, 0, ARG_PHRED64},
{(char*)"solexa1.3-quals", no_argument, 0, ARG_PHRED64},
{(char*)"chunkmbs", required_argument, 0, ARG_CHUNKMBS},
{(char*)"chunksz", required_argument, 0, ARG_CHUNKSZ},
{(char*)"chunkverbose", no_argument, 0, ARG_CHUNKVERBOSE},
{(char*)"mm", no_argument, 0, ARG_MM},
{(char*)"shmem", no_argument, 0, ARG_SHMEM},
{(char*)"mmsweep", no_argument, 0, ARG_MMSWEEP},
{(char*)"recal", no_argument, 0, ARG_RECAL},
{(char*)"pev2", no_argument, 0, ARG_PEV2},
{(char*)"refmap", required_argument, 0, ARG_REFMAP},
{(char*)"annotmap", required_argument, 0, ARG_ANNOTMAP},
{(char*)"reportse", no_argument, 0, ARG_REPORTSE},
{(char*)"hadoopout", no_argument, 0, ARG_HADOOPOUT},
{(char*)"fuzzy", no_argument, 0, ARG_FUZZY},
{(char*)"fullref", no_argument, 0, ARG_FULLREF},
{(char*)"usage", no_argument, 0, ARG_USAGE},
{(char*)"sam", no_argument, 0, 'S'},
{(char*)"sam-no-qname-trunc", no_argument, 0, ARG_SAM_NO_QNAME_TRUNC},
{(char*)"sam-nohead", no_argument, 0, ARG_SAM_NOHEAD},
{(char*)"sam-nosq", no_argument, 0, ARG_SAM_NOSQ},
{(char*)"sam-noSQ", no_argument, 0, ARG_SAM_NOSQ},
{(char*)"color", no_argument, 0, 'C'},
{(char*)"sam-RG", required_argument, 0, ARG_SAM_RG},
{(char*)"snpphred", required_argument, 0, ARG_SNPPHRED},
{(char*)"snpfrac", required_argument, 0, ARG_SNPFRAC},
{(char*)"suppress", required_argument, 0, ARG_SUPPRESS_FIELDS},
{(char*)"mapq", required_argument, 0, ARG_DEFAULT_MAPQ},
{(char*)"col-cseq", no_argument, 0, ARG_COLOR_SEQ},
{(char*)"col-cqual", no_argument, 0, ARG_COLOR_QUAL},
{(char*)"col-keepends", no_argument, 0, ARG_COLOR_KEEP_ENDS},
{(char*)"cost", no_argument, 0, ARG_COST},
{(char*)"showseed", no_argument, 0, ARG_SHOWSEED},
{(char*)"allow-contain",no_argument, 0, ARG_ALLOW_CONTAIN},
{(char*)"col-primer", no_argument, 0, ARG_COLOR_PRIMER},
{(char*)"wrapper", required_argument, 0, ARG_WRAPPER},
{(char*)0, 0, 0, 0} // terminator
};
/**
* Print a summary usage message to the provided output stream.
*/
static void printUsage(ostream& out) {
#ifdef BOWTIE_64BIT_INDEX
string tool_name = "bowtie-build-l";
#else
string tool_name = "bowtie-build-s";
#endif
if(wrapper == "basic-0") {
tool_name = "bowtie";
}
out << "Usage: " << endl
<< tool_name << " [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]" << endl
<< endl
<< " <m1> Comma-separated list of files containing upstream mates (or the" << endl
<< " sequences themselves, if -c is set) paired with mates in <m2>" << endl
<< " <m2> Comma-separated list of files containing downstream mates (or the" << endl
<< " sequences themselves if -c is set) paired with mates in <m1>" << endl
<< " <r> Comma-separated list of files containing Crossbow-style reads. Can be" << endl
<< " a mixture of paired and unpaired. Specify \"-\" for stdin." << endl
<< " <s> Comma-separated list of files containing unpaired reads, or the" << endl
<< " sequences themselves, if -c is set. Specify \"-\" for stdin." << endl
<< " <hit> File to write hits to (default: stdout)" << endl
<< "Input:" << endl
<< " -q query input files are FASTQ .fq/.fastq (default)" << endl
<< " -f query input files are (multi-)FASTA .fa/.mfa" << endl
<< " -r query input files are raw one-sequence-per-line" << endl
<< " -c query sequences given on cmd line (as <mates>, <singles>)" << endl
<< " -C reads and index are in colorspace" << endl
<< " -Q/--quals <file> QV file(s) corresponding to CSFASTA inputs; use with -f -C" << endl
<< " --Q1/--Q2 <file> same as -Q, but for mate files 1 and 2 respectively" << endl
<< " -s/--skip <int> skip the first <int> reads/pairs in the input" << endl
<< " -u/--qupto <int> stop after first <int> reads/pairs (excl. skipped reads)" << endl
<< " -5/--trim5 <int> trim <int> bases from 5' (left) end of reads" << endl
<< " -3/--trim3 <int> trim <int> bases from 3' (right) end of reads" << endl
<< " --phred33-quals input quals are Phred+33 (default)" << endl
<< " --phred64-quals input quals are Phred+64 (same as --solexa1.3-quals)" << endl
<< " --solexa-quals input quals are from GA Pipeline ver. < 1.3" << endl
<< " --solexa1.3-quals input quals are from GA Pipeline ver. >= 1.3" << endl
<< " --integer-quals qualities are given as space-separated integers (not ASCII)" << endl;
if(wrapper == "basic-0") {
out << " --large-index force usage of a 'large' index, even if a small one is present" << endl;
}
out << "Alignment:" << endl
<< " -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities" << endl
<< " or" << endl
<< " -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)" << endl
<< " -e/--maqerr <int> max sum of mismatch quals across alignment for -n (def: 70)" << endl
<< " -l/--seedlen <int> seed length for -n (default: 28)" << endl
<< " --nomaqround disable Maq-like quality rounding for -n (nearest 10 <= 30)" << endl
<< " -I/--minins <int> minimum insert size for paired-end alignment (default: 0)" << endl
<< " -X/--maxins <int> maximum insert size for paired-end alignment (default: 250)" << endl
<< " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)" << endl
<< " --nofw/--norc do not align to forward/reverse-complement reference strand" << endl
<< " --maxbts <int> max # backtracks for -n 2/3 (default: 125, 800 for --best)" << endl
<< " --pairtries <int> max # attempts to find mate for anchor hit (default: 100)" << endl
<< " -y/--tryhard try hard to find valid alignments, at the expense of speed" << endl
<< " --chunkmbs <int> max megabytes of RAM for best-first search frames (def: 64)" << endl
<< "Reporting:" << endl
<< " -k <int> report up to <int> good alignments per read (default: 1)" << endl
<< " -a/--all report all alignments per read (much slower than low -k)" << endl
<< " -m <int> suppress all alignments if > <int> exist (def: no limit)" << endl
<< " -M <int> like -m, but reports 1 random hit (MAPQ=0); requires --best" << endl
<< " --best hits guaranteed best stratum; ties broken by quality" << endl
<< " --strata hits in sub-optimal strata aren't reported (requires --best)" << endl
<< "Output:" << endl
<< " -t/--time print wall-clock time taken by search phases" << endl
<< " -B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)" << endl
<< " --quiet print nothing but the alignments" << endl
<< " --refout write alignments to files refXXXXX.map, 1 map per reference" << endl
<< " --refidx refer to ref. seqs by 0-based index rather than name" << endl
<< " --al <fname> write aligned reads/pairs to file(s) <fname>" << endl
<< " --un <fname> write unaligned reads/pairs to file(s) <fname>" << endl
<< " --max <fname> write reads/pairs over -m limit to file(s) <fname>" << endl
<< " --suppress <cols> suppresses given columns (comma-delim'ed) in default output" << endl
<< " --fullref write entire ref name (default: only up to 1st space)" << endl
<< "Colorspace:" << endl
<< " --snpphred <int> Phred penalty for SNP when decoding colorspace (def: 30)" << endl
<< " or" << endl
<< " --snpfrac <dec> approx. fraction of SNP bases (e.g. 0.001); sets --snpphred" << endl
<< " --col-cseq print aligned colorspace seqs as colors, not decoded bases" << endl
<< " --col-cqual print original colorspace quals, not decoded quals" << endl
<< " --col-keepends keep nucleotides at extreme ends of decoded alignment" << endl
<< "SAM:" << endl
<< " -S/--sam write hits in SAM format" << endl
<< " --mapq <int> default mapping quality (MAPQ) to print for SAM alignments" << endl
<< " --sam-nohead supppress header lines (starting with @) for SAM output" << endl
<< " --sam-nosq supppress @SQ header lines for SAM output" << endl
<< " --sam-RG <text> add <text> (usually \"lab=value\") to @RG line of SAM header" << endl
<< "Performance:" << endl
<< " -o/--offrate <int> override offrate of index; must be >= index's offrate" << endl
<< " -p/--threads <int> number of alignment threads to launch (default: 1)" << endl
#ifdef BOWTIE_MM
<< " --mm use memory-mapped I/O for index; many 'bowtie's can share" << endl
#endif
#ifdef BOWTIE_SHARED_MEM
<< " --shmem use shared mem for index; many 'bowtie's can share" << endl
#endif
<< "Other:" << endl
<< " --seed <int> seed for random number generator" << endl
<< " --verbose verbose output (for debugging)" << endl
<< " --version print version information and quit" << endl
<< " -h/--help print this usage message" << endl
;
if(wrapper.empty()) {
cerr << endl
<< "*** Warning ***" << endl
<< tool_name << " was run directly. It is recommended that you run the wrapper script 'bowtie' instead." << endl
<< endl;
}
}
/**
* Parse an int out of optarg and enforce that it be at least 'lower';
* if it is less than 'lower', than output the given error message and
* exit with an error and a usage message.
*/
static int parseInt(int lower, int upper, const char *errmsg, const char *arg) {
long l;
char *endPtr= NULL;
l = strtol(arg, &endPtr, 10);
if (endPtr != NULL) {
if (l < lower || l > upper) {
cerr << errmsg << endl;
printUsage(cerr);
throw 1;
}
return (int32_t)l;
}
cerr << errmsg << endl;
printUsage(cerr);
throw 1;
return -1;
}
/**
* Parse from optarg by default.
*/
static int parseInt(int lower, const char *errmsg) {
return parseInt(lower, INT_MAX, errmsg, optarg);
}
/**
* Upper is INT_MAX by default.
*/
static int parseInt(int lower, const char *errmsg, const char *arg) {
return parseInt(lower, INT_MAX, errmsg, arg);
}
/**
* Upper is INT_MAX, parse from optarg by default.
*/
static int parseInt(int lower, int upper, const char *errmsg) {
return parseInt(lower, upper, errmsg, optarg);
}
/**
* Parse a T string 'str'.
*/
template<typename T>
T parse(const char *s) {
T tmp;
stringstream ss(s);
ss >> tmp;
return tmp;
}
/**
* Parse a pair of Ts from a string, 'str', delimited with 'delim'.
*/
template<typename T>
pair<T, T> parsePair(const char *str, char delim) {
string s(str);
vector<string> ss;
tokenize(s, delim, ss);
pair<T, T> ret;
ret.first = parse<T>(ss[0].c_str());
ret.second = parse<T>(ss[1].c_str());
return ret;
}
/**
* Read command-line arguments
*/
static void parseOptions(int argc, const char **argv) {
int option_index = 0;
int next_option;
if(startVerbose) { cerr << "Parsing options: "; logTime(cerr, true); }
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 '1': tokenize(optarg, ",", mates1); break;
case '2': tokenize(optarg, ",", mates2); break;
case ARG_ONETWO: tokenize(optarg, ",", mates12); format = TAB_MATE; break;
case 'f': format = FASTA; break;
case 'F': {
format = FASTA_CONT;
pair<size_t, size_t> p = parsePair<size_t>(optarg, ',');
fastaContLen = p.first;
fastaContFreq = p.second;
break;
}
case 'q': format = FASTQ; break;
case 'r': format = RAW; break;
case 'c': format = CMDLINE; break;
case 'C': color = true; break;
case 'I':
minInsert = (uint32_t)parseInt(0, "-I arg must be positive");
break;
case 'X':
maxInsert = (uint32_t)parseInt(1, "-X arg must be at least 1");
break;
case 's':
skipReads = (uint32_t)parseInt(0, "-s arg must be positive");
break;
case ARG_FF: mate1fw = true; mate2fw = true; mateFwSet = true; break;
case ARG_RF: mate1fw = false; mate2fw = true; mateFwSet = true; break;
case ARG_FR: mate1fw = true; mate2fw = false; mateFwSet = true; break;
case ARG_RANDOM_READS: format = RANDOM; break;
case ARG_RANDOM_READS_NOSYNC:
format = RANDOM;
randReadsNoSync = true;
break;
case ARG_RANGE: rangeMode = true; break;
case ARG_CONCISE: outType = OUTPUT_CONCISE; break;
case 'S': outType = OUTPUT_SAM; break;
case ARG_REFOUT: refOut = true; break;
case ARG_NOOUT: outType = OUTPUT_NONE; break;
case ARG_REFMAP: refMapFile = optarg; break;
case ARG_ANNOTMAP: annotMapFile = optarg; break;
case ARG_SHMEM: useShmem = true; break;
case ARG_COLOR_SEQ: colorSeq = true; break;
case ARG_COLOR_QUAL: colorQual = true; break;
case ARG_SHOWSEED: showSeed = true; break;
case ARG_ALLOW_CONTAIN: gAllowMateContainment = true; break;
case ARG_COLOR_PRIMER: gReportColorPrimer = true; break;
case ARG_SUPPRESS_FIELDS: {
vector<string> supp;
tokenize(optarg, ",", supp);
for(size_t i = 0; i < supp.size(); i++) {
int ii = parseInt(1, "--suppress arg must be at least 1", supp[i].c_str());
suppressOuts.set(ii-1);
}
break;
}
case ARG_MM: {
#ifdef BOWTIE_MM
useMm = true;
break;
#else
cerr << "Memory-mapped I/O mode is disabled because bowtie was not compiled with" << endl
<< "BOWTIE_MM defined. Memory-mapped I/O is not supported under Windows. If you" << endl
<< "would like to use memory-mapped I/O on a platform that supports it, please" << endl
<< "refrain from specifying BOWTIE_MM=0 when compiling Bowtie." << endl;
throw 1;
#endif
}
case ARG_MMSWEEP: mmSweep = true; break;
case ARG_HADOOPOUT: hadoopOut = true; break;
case ARG_AL: dumpAlBase = optarg; break;
case ARG_UN: dumpUnalBase = optarg; break;
case ARG_MAXDUMP: dumpMaxBase = optarg; break;
case ARG_SOLEXA_QUALS: solexaQuals = true; break;
case ARG_integerQuals: integerQuals = true; break;
case ARG_PHRED64: phred64Quals = true; break;
case ARG_PHRED33: solexaQuals = false; phred64Quals = false; break;
case ARG_NOMAQROUND: noMaqRound = true; break;
case ARG_COLOR_KEEP_ENDS: colorExEnds = false; break;
case ARG_SNPPHRED: snpPhred = parseInt(0, "--snpphred must be at least 0"); break;
case ARG_SNPFRAC: {
double p = parse<double>(optarg);
if(p <= 0.0) {
cerr << "Error: --snpfrac parameter must be > 0.0" << endl;
throw 1;
}
p = (log10(p) * -10);
snpPhred = (int)(p + 0.5);
if(snpPhred < 10)
cout << "snpPhred: " << snpPhred << endl;
break;
}
case 'z': {
cerr << "Error: -z/--phased mode is no longer supported" << endl;
throw 1;
}
case ARG_REFIDX: noRefNames = true; break;
case ARG_STATEFUL: stateful = true; break;
case ARG_FUZZY: fuzzy = true; break;
case ARG_REPORTSE: reportSe = true; break;
case ARG_FULLREF: fullRef = true; break;
case ARG_PREFETCH_WIDTH:
prefetchWidth = parseInt(1, "--prewidth must be at least 1");
break;
case 'B':
offBase = parseInt(-999999, "-B/--offbase cannot be a large negative number");
break;
case ARG_SEED:
seed = parseInt(0, "--seed arg must be at least 0");
break;
case 'u':
qUpto = (uint32_t)parseInt(1, "-u/--qupto arg must be at least 1");
break;
case 'k':
khits = (uint32_t)parseInt(1, "-k arg must be at least 1");
break;
case 'Q':
tokenize(optarg, ",", qualities);
integerQuals = true;
break;
case ARG_QUALS1:
tokenize(optarg, ",", qualities1);
integerQuals = true;
break;
case ARG_QUALS2:
tokenize(optarg, ",", qualities2);
integerQuals = true;
break;
case 'M':
sampleMax = true;
case 'm':
mhits = (uint32_t)parseInt(1, "-m arg must be at least 1");
break;
case 'x':
mixedThresh = (uint32_t)parseInt(0, "-x arg must be at least 0");
break;
case ARG_MIXED_ATTEMPTS:
mixedAttemptLim = (uint32_t)parseInt(1, "--pairtries arg must be at least 1");
break;
case ARG_CACHE_LIM:
cacheLimit = (uint32_t)parseInt(1, "--cachelim arg must be at least 1");
break;
case ARG_CACHE_SZ:
cacheSize = (uint32_t)parseInt(1, "--cachesz arg must be at least 1");
cacheSize *= (1024 * 1024); // convert from MB to B
break;
case ARG_NO_RECONCILE:
dontReconcileMates = true;
break;
case 'p':
nthreads = parseInt(1, "-p/--threads arg must be at least 1");
break;
case ARG_FILEPAR:
fileParallel = true;
break;
case 'v':
maqLike = 0;
mismatches = parseInt(0, 3, "-v arg must be at least 0 and at most 3");
break;
case '3': trim3 = parseInt(0, "-3/--trim3 arg must be at least 0"); break;
case '5': trim5 = parseInt(0, "-5/--trim5 arg must be at least 0"); break;
case 'o': offRate = parseInt(1, "-o/--offrate arg must be at least 1"); break;
case ARG_ISARATE: isaRate = parseInt(0, "--isarate arg must be at least 0"); break;
case 'e': qualThresh = parseInt(1, "-e/--err arg must be at least 1"); break;
case 'n': seedMms = parseInt(0, 3, "-n/--seedmms arg must be at least 0 and at most 3"); maqLike = 1; break;
case 'l': seedLen = parseInt(5, "-l/--seedlen arg must be at least 5"); break;
case 'h': printUsage(cout); throw 0; break;
case ARG_USAGE: printUsage(cout); throw 0; break;
case 'a': allHits = true; break;
case 'y': tryHard = true; break;
case ARG_RECAL: recal = true; break;
case ARG_CHUNKMBS: chunkPoolMegabytes = parseInt(1, "--chunkmbs arg must be at least 1"); break;
case ARG_CHUNKSZ: chunkSz = parseInt(1, "--chunksz arg must be at least 1"); break;
case ARG_CHUNKVERBOSE: chunkVerbose = true; break;
case ARG_BETTER: stateful = true; better = true; break;
case ARG_BEST: stateful = true; useV1 = false; break;
case ARG_STRATA: strata = true; break;
case ARG_VERBOSE: verbose = true; break;
case ARG_STARTVERBOSE: startVerbose = true; break;
case ARG_QUIET: quiet = true; break;
case ARG_SANITY: sanityCheck = true; break;
case 't': timing = true; break;
case ARG_NO_FW: nofw = true; break;
case ARG_NO_RC: norc = true; break;
case ARG_STATS: stats = true; break;
case ARG_PEV2: useV1 = false; break;
case ARG_SAM_NO_QNAME_TRUNC: samNoQnameTrunc = true; break;
case ARG_SAM_NOHEAD: samNoHead = true; break;
case ARG_SAM_NOSQ: samNoSQ = true; break;
case ARG_SAM_RG: {
if(!rgs.empty()) rgs += '\t';
rgs += optarg;
break;
}
case ARG_COST: printCost = true; break;
case ARG_DEFAULT_MAPQ:
defaultMapq = parseInt(0, "--mapq must be positive");
break;
case ARG_MAXBTS: {
maxBts = parseInt(0, "--maxbts must be positive");
maxBtsBetter = maxBts;
break;
}
case ARG_DUMP_PATS: patDumpfile = optarg; break;
case ARG_STRAND_FIX: strandFix = true; break;
case ARG_RANDOMIZE_QUALS: randomizeQuals = true; break;
case ARG_PARTITION: partitionSz = parse<int>(optarg); break;
case ARG_ORIG:
if(optarg == NULL || strlen(optarg) == 0) {
cerr << "--orig arg must be followed by a string" << endl;
printUsage(cerr);
throw 1;
}
origString = optarg;
break;
case -1: break; /* Done with options. */
case 0:
if (long_options[option_index].flag != 0)
break;
default:
printUsage(cerr);
throw 1;
}
} while(next_option != -1);
bool paired = mates1.size() > 0 || mates2.size() > 0 || mates12.size() > 0;
if(rangeMode) {
// Tell the Ebwt loader to ignore the suffix-array portion of
// the index. We don't need it because the user isn't asking
// for bowtie to report reference positions (just matrix
// ranges).
offRate = 32;
}
if(!maqLike && mismatches == 3) {
// Much faster than normal 3-mismatch mode
stateful = true;
}
if(mates1.size() != mates2.size()) {
cerr << "Error: " << mates1.size() << " mate files/sequences were specified with -1, but " << mates2.size() << endl
<< "mate files/sequences were specified with -2. The same number of mate files/" << endl
<< "sequences must be specified with -1 and -2." << endl;
throw 1;
}
if(qualities.size() && format != FASTA) {
cerr << "Error: one or more quality files were specified with -Q but -f was not" << endl
<< "enabled. -Q works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities.size() && !color) {
cerr << "Error: one or more quality files were specified with -Q but -C was not" << endl
<< "enabled. -Q works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities1.size() && format != FASTA) {
cerr << "Error: one or more quality files were specified with --Q1 but -f was not" << endl
<< "enabled. --Q1 works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities1.size() && !color) {
cerr << "Error: one or more quality files were specified with --Q1 but -C was not" << endl
<< "enabled. --Q1 works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities2.size() && format != FASTA) {
cerr << "Error: one or more quality files were specified with --Q2 but -f was not" << endl
<< "enabled. --Q2 works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities2.size() && !color) {
cerr << "Error: one or more quality files were specified with --Q2 but -C was not" << endl
<< "enabled. --Q2 works only in combination with -f and -C." << endl;
throw 1;
}
if(qualities1.size() > 0 && mates1.size() != qualities1.size()) {
cerr << "Error: " << mates1.size() << " mate files/sequences were specified with -1, but " << qualities1.size() << endl
<< "quality files were specified with --Q1. The same number of mate and quality" << endl
<< "files must sequences must be specified with -1 and --Q1." << endl;
throw 1;
}
if(qualities2.size() > 0 && mates2.size() != qualities2.size()) {
cerr << "Error: " << mates2.size() << " mate files/sequences were specified with -2, but " << qualities2.size() << endl
<< "quality files were specified with --Q2. The same number of mate and quality" << endl
<< "files must sequences must be specified with -2 and --Q2." << endl;
throw 1;
}
// Check for duplicate mate input files
if(format != CMDLINE) {
for(size_t i = 0; i < mates1.size(); i++) {
for(size_t j = 0; j < mates2.size(); j++) {
if(mates1[i] == mates2[j] && !quiet) {
cerr << "Warning: Same mate file \"" << mates1[i] << "\" appears as argument to both -1 and -2" << endl;
}
}
}
}
if(tryHard) {
// Increase backtracking limit to huge number
maxBts = maxBtsBetter = INT_MAX;
// Increase number of paired-end scan attempts to huge number
mixedAttemptLim = UINT_MAX;
}
if(!stateful && sampleMax) {
if(!quiet) {
cerr << "Warning: -M was specified w/o --best; automatically enabling --best" << endl;
}
stateful = true;
}
if(strata && !stateful) {
cerr << "--strata must be combined with --best" << endl;
throw 1;
}
if(strata && !allHits && khits == 1 && mhits == 0xffffffff) {
cerr << "--strata has no effect unless combined with -m, -a, or -k N where N > 1" << endl;
throw 1;
}
if(fuzzy && (!stateful && !paired)) {
cerr << "--fuzzy must be combined with --best or paired-end alignment" << endl;
throw 1;
}
// If both -s and -u are used, we need to adjust qUpto accordingly
// since it uses patid to know if we've reached the -u limit (and
// patids are all shifted up by skipReads characters)
if(qUpto + skipReads > qUpto) {
qUpto += skipReads;
}
if(useShmem && useMm && !quiet) {
cerr << "Warning: --shmem overrides --mm..." << endl;
useMm = false;
}
if(snpPhred <= 10 && color && !quiet) {
cerr << "Warning: the colorspace SNP penalty (--snpphred) is very low: " << snpPhred << endl;
}
if(outType == OUTPUT_SAM && refOut) {
cerr << "Error: --refout cannot be combined with -S/--sam" << endl;
throw 1;
}
if(!mateFwSet) {
if(color) {
// Set colorspace default (--ff)
mate1fw = true;
mate2fw = true;
} else {
// Set nucleotide space default (--fr)
mate1fw = true;
mate2fw = false;
}
}
if(outType != OUTPUT_FULL && suppressOuts.count() > 0 && !quiet) {
cerr << "Warning: Ignoring --suppress because output type is not default." << endl;