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swipe.cc
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/*
SWIPE
Smith-Waterman database searches with Inter-sequence Parallel Execution
Copyright (C) 2008-2014 Torbjorn Rognes, University of Oslo,
Oslo University Hospital and Sencel Bioinformatics AS
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Contact: Torbjorn Rognes <[email protected]>,
Department of Informatics, University of Oslo,
PO Box 1080 Blindern, NO-0316 Oslo, Norway
*/
#include "swipe.h"
/* ARGUMENTS AND THEIR DEFAULTS */
#define DEFAULT_MAXMATCHES 250
#define DEFAULT_ALIGNMENTS 100
#define DEFAULT_MINSCORE 1
#define DEFAULT_MAXSCORE (LONG_MAX)
#define DEFAULT_QUERYNAME "-"
#define DEFAULT_DATABASENAME ""
#define DEFAULT_GAPOPEN 0
#define DEFAULT_GAPEXTEND 0
#define DEFAULT_MATRIXNAME "BLOSUM62"
#define DEFAULT_MATCHSCORE 1
#define DEFAULT_MISMATCHSCORE (-3)
#define DEFAULT_THREADS 1
#define DEFAULT_VIEW 0
#define DEFAULT_SYMTYPE 1
#define DEFAULT_SHOW_GIS 0
#define DEFAULT_SHOW_TAXID 0
#define DEFAULT_EXPECT 10.0
#define DEFAULT_MINEXPECT 0.0
#define DEFAULT_QUERYSTRANDS 3
#define DEFAULT_QUERY_GENCODE 1
#define DEFAULT_DB_GENCODE 1
#define DEFAULT_SUBALIGNMENTS 1
#define DEFAULT_DUMP 0
#define DEFAULT_OUT stdout
#define DEFAULT_EFFDBSIZE 0
char * progname;
const char * matrixname;
const char * databasename;
const char * queryname;
char * taxidfilename;
char * outfile = NULL;
double expect;
double minexpect;
long minscore;
long maxscore;
long alignments;
long maxmatches;
long gapopen;
long gapextend;
long threads;
long view;
long symtype;
long show_gis;
long show_taxid;
long matchscore;
long mismatchscore;
long gapopenextend;
long querystrands;
long query_gencode;
long db_gencode;
long subalignments;
long dump;
long effdbsize;
/* Other variables */
long queryno;
long cpu_feature_sse2;
long cpu_feature_ssse3;
long cpu_feature_sse41;
#define MAX_THREADS 256
pthread_mutex_t countmutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_t workmutex = PTHREAD_MUTEX_INITIALIZER;
pthread_t pthread_id[MAX_THREADS];
#ifdef MPISWIPE
int mpirank, mpisize;
#endif
long maxchunksize;
long volnext;
long seqnext;
long * volchunks;
long * volseqs;
long compute7;
long compute16;
long compute32;
long compute63;
long rounds7;
long rounds16;
long rounds32;
long rounds63;
long totalhits;
FILE * out = stdout;
struct time_info ti;
struct search_data
{
struct db_thread_s * dbt;
struct db_thread_s * dbta[8];
BYTE * dprofile;
BYTE * hearray;
BYTE ** qtable[6];
long * scores;
long * bestpos;
long * bestq;
long * start_list;
long * in_list;
long * out_list;
long * tmp_list;
long qlen[6];
long start_count;
long in_count;
long out_count;
long * start_hits;
long seqfirst, seqlast;
long qstrand1, qstrand2, qframe1, qframe2;
long dstrand1, dstrand2, dframe1, dframe2;
};
void fatal(const char * message)
{
if (message)
fprintf(stderr, "%s\n", message);
exit(1);
}
void fatal(const char * format, const char * message)
{
fprintf(stderr, format, message);
fprintf(stderr, "\n");
exit(1);
}
void * xmalloc(size_t size)
{
const size_t alignment = 16;
void * t = NULL;
posix_memalign(& t, alignment, size);
if (t==NULL)
fatal("Unable to allocate enough memory.");
return t;
}
void * xrealloc(void *ptr, size_t size)
{
void * t = realloc(ptr, size);
if (!t)
fatal("Unable to allocate enough memory.");
return t;
}
long alignedhits;
long alignedall;
long * hits_sorted;
long align_volnext;
long align_seqnext;
long * align_volseqs;
long * align_volchunks;
void align_init(struct search_data * sdp)
{
sdp->dbt = db_thread_create();
for(int i=0; i<8; i++)
sdp->dbta[i] = db_thread_create();
sdp->dprofile = (BYTE*) xmalloc(4*16*32);
long qlen = 0;
long hearraylen = 0;
for(int i = 0; i < 6; i++)
{
sdp->qtable[i] = 0;
}
if (symtype == 0)
{
for(int s=0; s<2; s++)
if ((s+1) & querystrands)
{
qlen = query.nt[s].len;
sdp->qlen[3*s] = qlen;
sdp->qtable[3*s] = (BYTE**) xmalloc(qlen*sizeof(BYTE*));
for(int i=0; i<qlen; i++)
{
sdp->qtable[3*s][i] = sdp->dprofile + 16*query.nt[s].seq[i];
}
hearraylen = qlen > hearraylen ? qlen : hearraylen;
}
}
else if ((symtype == 1) || (symtype == 3) || (symtype == 5))
{
qlen = query.aa[0].len;
sdp->qlen[0] = qlen;
sdp->qtable[0] = (BYTE**) xmalloc(qlen*sizeof(BYTE*));
for(int i=0; i<qlen; i++)
{
sdp->qtable[0][i] = sdp->dprofile + 16*query.aa[0].seq[i];
}
hearraylen = qlen > hearraylen ? qlen : hearraylen;
}
else if ((symtype == 2) || (symtype == 4))
{
for(int s=0; s<2; s++)
if ((s+1) & querystrands)
for(int f=0; f<3; f++)
{
qlen = query.aa[3*s+f].len;
sdp->qlen[3*s+f] = qlen;
sdp->qtable[3*s+f] = (BYTE**) xmalloc(qlen*sizeof(BYTE*));
for(int i=0; i<qlen; i++)
{
sdp->qtable[3*s+f][i] = sdp->dprofile + 16*query.aa[3*s+f].seq[i];
}
hearraylen = qlen > hearraylen ? qlen : hearraylen;
}
}
// fprintf(out, "hearray length = %ld\n", hearraylen);
sdp->hearray = (BYTE*) xmalloc(hearraylen*32);
long listsize = maxchunksize * sizeof(long);
// if ((symtype == 3) || (symtype == 4))
// listsize *= 6;
sdp->start_list = (long*) xmalloc(listsize);
sdp->start_hits = (long*) xmalloc(listsize);
sdp->in_list = (long*) xmalloc(listsize);
sdp->out_list = (long*) xmalloc(listsize);
sdp->scores = (long*) xmalloc(listsize);
sdp->bestpos = (long*) xmalloc(listsize);
sdp->bestq = (long*) xmalloc(listsize);
if (symtype == 0)
{
sdp->qstrand1 = querystrands == 2 ? 1 : 0;
sdp->qframe1 = 0;
sdp->qstrand2 = querystrands == 1 ? 0 : 1;
sdp->qframe2 = 0;
sdp->dstrand1 = 0;
sdp->dframe1 = 0;
sdp->dstrand2 = 0;
sdp->dframe2 = 0;
}
else if (symtype == 2)
{
sdp->qstrand1 = querystrands == 2 ? 1 : 0;
sdp->qframe1 = 0;
sdp->qstrand2 = querystrands == 1 ? 0 : 1;
sdp->qframe2 = 2;
sdp->dstrand1 = 0;
sdp->dframe1 = 0;
sdp->dstrand2 = 0;
sdp->dframe2 = 0;
}
else if (symtype == 3)
{
sdp->qstrand1 = 0;
sdp->qframe1 = 0;
sdp->qstrand2 = 0;
sdp->qframe2 = 0;
sdp->dstrand1 = 0;
sdp->dframe1 = 0;
sdp->dstrand2 = 1;
sdp->dframe2 = 2;
}
else if (symtype == 4)
{
sdp->qstrand1 = querystrands == 2 ? 1 : 0;
sdp->qframe1 = 0;
sdp->qstrand2 = querystrands == 1 ? 0 : 1;
sdp->qframe2 = 2;
sdp->dstrand1 = 0;
sdp->dframe1 = 0;
sdp->dstrand2 = 1;
sdp->dframe2 = 2;
}
else
{
sdp->qstrand1 = 0;
sdp->qframe1 = 0;
sdp->qstrand2 = 0;
sdp->qframe2 = 0;
sdp->dstrand1 = 0;
sdp->dframe1 = 0;
sdp->dstrand2 = 0;
sdp->dframe2 = 0;
}
}
void align_chunk(struct search_data * sdp, long hitfirst, long hitlast)
{
if (hitlast < alignments)
{
for (long qstrand = sdp->qstrand1; qstrand <= sdp->qstrand2; qstrand++)
for(long qframe = sdp->qframe1; qframe <= sdp->qframe2; qframe++)
{
sdp->start_count = 0;
for(long hitno = hitfirst; hitno <= hitlast; hitno++)
{
long hs = hits_sorted[hitno];
long seqno, score, hqstrand, hqframe, hdstrand, hdframe;
hits_gethit(hs, & seqno, & score, & hqstrand, & hqframe,
& hdstrand, & hdframe);
if ((qstrand == hqstrand) && (qframe == hqframe))
{
sdp->start_hits[sdp->start_count] = hs;
sdp->start_list[sdp->start_count] =
(seqno << 3) | (hdstrand << 2) | hdframe;
sdp->start_count++;
}
}
if (sdp->start_count)
{
// printf("Aligning %ld sequences.\n", sdp->start_count);
BYTE ** qtable = sdp->qtable[3*qstrand+qframe];
long qlen = sdp->qlen[3*qstrand+qframe];
/* 16-bit search, 8x1 db symbols, with alignment end */
pthread_mutex_lock(&countmutex);
compute32 += sdp->in_count;
rounds32++;
pthread_mutex_unlock(&countmutex);
search16s((WORD**)qtable,
gapopenextend,
gapextend,
(WORD*)(score_matrix_16),
(WORD*)(sdp->dprofile),
(WORD*)(sdp->hearray),
sdp->dbta,
sdp->start_count,
sdp->start_list,
sdp->scores,
sdp->bestpos,
sdp->bestq,
qlen);
for (int i=0; i<sdp->start_count; i++)
{
long pos = sdp->bestpos[i];
long bestq = sdp->bestq[i];
// fprintf(out, "seqno=%ld score=%ld bestpos=%ld\n", seqno, score, pos);
long hitno = sdp->start_hits[i];
if (sdp->scores[i] < SCORELIMIT_16)
hits_enter_align_hint(hitno, bestq, pos);
}
}
}
}
for(long hitno = hitfirst; hitno <= hitlast; hitno++)
hits_align(sdp->dbt, hits_sorted[hitno]);
}
void align_done(struct search_data * sdp)
{
for(int i = 0; i < 6; i++)
{
if (sdp->qtable[i])
free(sdp->qtable[i]);
}
free(sdp->dprofile);
free(sdp->hearray);
free(sdp->scores);
free(sdp->bestpos);
free(sdp->bestq);
free(sdp->start_list);
free(sdp->start_hits);
free(sdp->in_list);
free(sdp->out_list);
for(int i=0; i<8; i++)
db_thread_destruct(sdp->dbta[i]);
db_thread_destruct(sdp->dbt);
}
void calc_chunks(long volcount,
long par,
long channels,
long * volseqs,
long * volchunks,
long * totalchunks,
long * biggestchunk)
{
#ifdef DEBUG
fprintf(out, "Calculating chunk distribution among volumes\n");
#endif
long volsused = 0;
long chunksizes[volcount];
long totalseqs = 0;
long maxchunksize = 0;
long vv = 0;
for(long v = 0; v < volcount; v++)
{
if (volseqs[v])
{
totalseqs += volseqs[v];
volsused++;
volchunks[v] = 1;
chunksizes[v] = volseqs[v];
if (chunksizes[v] > maxchunksize)
{
maxchunksize = chunksizes[v];
vv = v;
}
}
else
{
chunksizes[v] = 0;
volchunks[v] = 0;
}
}
long upper = channels;
if (totalseqs >= 4 * channels * par)
upper *= (long) (floor(sqrt((1.0 * totalseqs) / (channels * par))));
long chunks = volsused;
long minchunks = totalseqs < par ? totalseqs : par;
while((maxchunksize > upper) || (chunks < minchunks))
{
volchunks[vv]++;
chunks++;
chunksizes[vv] = (volseqs[vv] + volchunks[vv] - 1) / volchunks[vv];
maxchunksize = 0;
vv = 0;
for(long v=0; v < volcount; v++)
{
if (chunksizes[v] > maxchunksize)
{
vv = v;
maxchunksize = chunksizes[v];
}
}
}
#ifdef DEBUG
#ifdef MPISWIPE
if (!mpirank)
#endif
{
fprintf(out, "\n");
fprintf(out, "Chunk distribution:\n");
fprintf(out, "Total seqs: %ld\n", totalseqs);
fprintf(out, "Total chunks: %ld Upper size limit: %ld\n", chunks, upper);
fprintf(out, "Vol Sequences Chunks Maxchunksize\n");
for(long v = 0; v < volcount; v++)
{
fprintf(out, "%3ld %9ld %6ld %12ld\n",
v, volseqs[v], volchunks[v], chunksizes[v]);
}
fprintf(out, "\n");
}
#endif
*biggestchunk = maxchunksize;
*totalchunks = chunks;
}
void align_threads_init()
{
long hits = hits_getcount();
hits_sorted = hits_sort();
long bins = 7;
align_volseqs = (long*) xmalloc(bins*sizeof(long));
align_volchunks = (long*) xmalloc(bins*sizeof(long));
for(long i = 0; i<bins; i++)
align_volseqs[i] = 0;
for(long i = 0; i<hits; i++)
{
long seqno;
long score;
long qstrand;
long qframe;
long dstrand;
long dframe;
if (i>=alignments)
align_volseqs[6]++;
else
{
hits_gethit(i, & seqno, & score,
& qstrand, & qframe,
& dstrand, & dframe);
align_volseqs[3*qstrand+qframe]++;
}
}
long totalchunks;
calc_chunks(bins,
threads,
8,
align_volseqs,
align_volchunks,
& totalchunks,
& maxchunksize);
alignedhits = 0;
align_volnext = 0;
while ((align_volnext < bins) && (align_volchunks[align_volnext] == 0))
align_volnext++;
}
void align_threads_done()
{
free(hits_sorted);
free(align_volchunks);
free(align_volseqs);
}
int align_getwork(long * first, long * last)
{
int status = 0;
long bins = 7;
long volcount = bins;
pthread_mutex_lock(&workmutex);
if (align_volnext < volcount)
{
long seqcount = align_volseqs[align_volnext];
long chunks = align_volchunks[align_volnext];
long chunksize = ((seqcount+chunks-1) / chunks);
* first = alignedhits;
* last = alignedhits + chunksize - 1;
alignedhits += chunksize;
status = 1;
align_volseqs[align_volnext] -= chunksize;
align_volchunks[align_volnext]--;
while ((align_volnext < bins) && (align_volchunks[align_volnext] == 0))
align_volnext++;
}
pthread_mutex_unlock(&workmutex);
return status;
}
void * align_worker(void *)
{
search_data sd;
align_init(&sd);
long i, j;
while(align_getwork(&i, &j))
align_chunk(&sd, i, j);
align_done(&sd);
return 0;
}
void align_threads()
{
long t;
void * status;
align_threads_init();
for(t=0; t<threads; t++)
{
if (pthread_create(pthread_id + t, 0, align_worker, (void *)t))
fatal("Cannot create thread.");
}
for(t=0; t<threads; t++) {
if (pthread_join(pthread_id[t], &status))
fatal("Cannot join thread.");
}
align_threads_done();
}
void args_getstring(int i, int argc, char **argv, char ** result, char * error)
{
if (i+1 < argc)
*result = argv[i+1];
else
fatal(error);
}
void args_getnum(int i, int argc, char **argv, long * result, char * error)
{
if (i+1 < argc)
*result = atol(argv[i+1]);
else
fatal(error);
}
void args_show()
{
if (view == 0)
{
#ifndef MPISWIPE
if (! cpu_feature_ssse3)
{
fprintf(out, "The performance is reduced because this CPU lacks SSSE3.\n\n");
}
#endif
const char * symtypestring[] = { "Nucleotide", "Amino acid", "Translated query", "Translated database", "Both translated", "Sound" };
// char * viewtypestring[] = { "plain", 0, 0, 0, 0, 0, 0, "xml",
// "tab-separated", "tab-separated with comments" };
fprintf(out, "Database file: %s\n", databasename);
fprintf(out, "Database title: %s\n", db_gettitle());
fprintf(out, "Database time: %s\n", db_gettime());
if (db_ismasked())
{
fprintf(out, "Database size: %ld residues", db_getsymcount_masked());
fprintf(out, " in %ld sequences\n", db_getseqcount_masked());
}
else
{
fprintf(out, "Database size: %ld residues", db_getsymcount());
fprintf(out, " in %ld sequences\n", db_getseqcount());
}
fprintf(out, "Longest db seq: %ld residues\n", db_getlongest());
if (effdbsize > 0)
fprintf(out, "Effecive db size: %ld\n", effdbsize);
fprintf(out, "Query file name: %s\n", queryname);
long qlen;
if ((symtype == 0) || (symtype == 2) || (symtype == 4))
qlen = query.nt[0].len;
else
qlen = query.aa[0].len;
fprintf(out, "Query length: %ld residues\n", qlen);
query_show();
if (symtype == 0)
{
fprintf(out, "Query strands: ");
switch (querystrands)
{
case 1:
fprintf(out, "Plus");
break;
case 2:
fprintf(out, "Minus");
break;
case 3:
fprintf(out, "Plus and minus");
break;
}
fprintf(out, "\n");
fprintf(out, "Score matrix: %ld/%ld\n", matchscore, mismatchscore);
}
else
{
fprintf(out, "Score matrix: %s\n", matrixname);
}
fprintf(out, "Gap penalty: %ld+%ldk\n", gapopen, gapextend);
fprintf(out, "Max expect shown: %-g\n", expect);
fprintf(out, "Min score shown: %ld\n", minscore);
fprintf(out, "Max matches shown: %ld\n", maxmatches);
fprintf(out, "Alignments shown: %ld\n", alignments);
fprintf(out, "Show gi's: %ld\n", show_gis);
fprintf(out, "Show taxid's: %ld\n", show_taxid);
fprintf(out, "Threads: %ld\n", threads);
fprintf(out, "Symbol type: %s\n", symtypestring[symtype]);
if ((symtype == 2) || (symtype == 4))
fprintf(out, "Query genetic code:%s (%ld)\n", gencode_names[query_gencode-1], query_gencode);
if ((symtype == 3) || (symtype == 4))
fprintf(out, "DB genetic code: %s (%ld)\n", gencode_names[db_gencode-1], db_gencode);
#if 0
if ((symtype == 2) || (symtype == 4))
{
for(long s=0; s<2; s++)
for(long f=0; f<3; f++)
{
fprintf(out, "Translation of query, frame %c%ld:\n", s?'-':'+', f+1);
// translate(query_, qlen, s, f, 0, & prot, & plen);
long plen = query.aa[3*s+f].len;
for (int j=0; j<plen; j+=60)
{
for(int k=0; k<60; k++)
{
if (j+k < plen)
putc(sym_ncbi_aa[query.aa[3*s+f].seq[j+k]], out);
else
break;
}
fprintf(out, "\n");
}
fprintf(out, "\n");
}
}
#endif
// fprintf(out, "View: %s\n", viewtypestring[view]);
if (taxidfilename)
fprintf(out, "Taxid filename: %s\n", taxidfilename);
fprintf(out, "\n");
}
}
void args_usage()
{
/* options unused by BLAST: chkuxHN */
/* options used by SWIPE: chkuxHN */
fprintf(out, "Usage: %s [OPTIONS]\n", progname);
fprintf(out, " -h, --help show help\n");
fprintf(out, " -d, --db=FILE sequence database base name (required)\n");
fprintf(out, " -i, --query=FILE query sequence filename (stdin)\n");
fprintf(out, " -M, --matrix=NAME/FILE score matrix name or filename (BLOSUM62)\n");
fprintf(out, " -q, --penalty=NUM penalty for nucleotide mismatch (-3)\n");
fprintf(out, " -r, --reward=NUM reward for nucleotide match (1)\n");
fprintf(out, " -G, --gapopen=NUM gap open penalty (11)\n");
fprintf(out, " -E, --gapextend=NUM gap extension penalty (1)\n");
fprintf(out, " -v, --num_descriptions=NUM sequence descriptions to show (250)\n");
fprintf(out, " -b, --num_alignments=NUM sequence alignments to show (100)\n");
fprintf(out, " -e, --evalue=REAL maximum expect value of sequences to show (10.0)\n");
fprintf(out, " -k, --minevalue=REAL minimum expect value of sequences to show (0.0)\n");
fprintf(out, " -c, --min_score=NUM minimum score of sequences to show (1)\n");
fprintf(out, " -u, --max_score=NUM maximum score of sequences to show (inf.)\n");
fprintf(out, " -a, --num_threads=NUM number of threads to use [1-%d] (1)\n", MAX_THREADS);
fprintf(out, " -m, --outfmt=NUM output format [0,7-9=plain,xml,tsv,tsv+] (0)\n");
fprintf(out, " -I, --show_gis show gi numbers in results (no)\n");
fprintf(out, " -p, --symtype=NAME/NUM symbol type/translation [0-4] (1)\n");
fprintf(out, " -S, --strand=NAME/NUM query strands to search [1-3] (3)\n");
fprintf(out, " -Q, --query_gencode=NUM query genetic code [1-23] (1)\n");
fprintf(out, " -D, --db_gencode=NUM database genetic code [1-23] (1)\n");
fprintf(out, " -x, --taxidlist=FILE taxid list filename (none)\n");
fprintf(out, " -N, --dump=NUM dump database [0-2=no,yes,split headers] (0)\n");
fprintf(out, " -H, --show_taxid show taxid etc in results (no)\n");
fprintf(out, " -o, --out=FILE output file (stdout)\n");
fprintf(out, " -z, --dbsize=NUM set effective database size (0)\n");
}
void args_help()
{
char title[] = "SWIPE " SWIPE_VERSION;
char ref[] = "Reference: T. Rognes (2011) Faster Smith-Waterman database searches\nwith inter-sequence SIMD parallelisation, BMC Bioinformatics, 12:221.";
fprintf(out, "%s [%s %s]\n\n%s\n\n", title, __DATE__, __TIME__, ref);
args_usage();
}
void args_init(int argc, char **argv)
{
/* Set defaults */
gapopen = DEFAULT_GAPOPEN;
gapextend = DEFAULT_GAPEXTEND;
matrixname = "";
queryname = DEFAULT_QUERYNAME;
databasename = DEFAULT_DATABASENAME;
minscore = DEFAULT_MINSCORE;
maxscore = DEFAULT_MAXSCORE;
maxmatches = DEFAULT_MAXMATCHES;
alignments = DEFAULT_ALIGNMENTS;
threads = DEFAULT_THREADS;
view = DEFAULT_VIEW;
symtype = DEFAULT_SYMTYPE;
show_gis = DEFAULT_SHOW_GIS;
show_taxid = DEFAULT_SHOW_TAXID;
expect = DEFAULT_EXPECT;
minexpect = DEFAULT_MINEXPECT;
taxidfilename = NULL;
matchscore = DEFAULT_MATCHSCORE;
mismatchscore = DEFAULT_MISMATCHSCORE;
querystrands = DEFAULT_QUERYSTRANDS;
query_gencode = DEFAULT_QUERY_GENCODE;
db_gencode = DEFAULT_DB_GENCODE;
subalignments = DEFAULT_SUBALIGNMENTS;
dump = DEFAULT_DUMP;
effdbsize = DEFAULT_EFFDBSIZE;
progname = argv[0];
opterr = 1;
char short_options[] = "d:i:M:q:r:G:E:S:v:b:c:u:e:k:a:m:p:x:C:Q:D:F:K:N:o:z:IHh";
static struct option long_options[] =
{
{"db", required_argument, NULL, 'd' },
{"query", required_argument, NULL, 'i' },
{"matrix", required_argument, NULL, 'M' },
{"penalty", required_argument, NULL, 'q' },
{"reward", required_argument, NULL, 'r' },
{"gapopen", required_argument, NULL, 'G' },
{"gapextend", required_argument, NULL, 'E' },
{"strand", required_argument, NULL, 'S' },
{"num_descriptions", required_argument, NULL, 'v' },
{"num_alignments", required_argument, NULL, 'b' },
{"min_score", required_argument, NULL, 'c' },
{"max_score", required_argument, NULL, 'u' },
{"evalue", required_argument, NULL, 'e' },
{"minevalue", required_argument, NULL, 'k' },
{"num_threads", required_argument, NULL, 'a' },
{"outfmt", required_argument, NULL, 'm' },
{"symtype", required_argument, NULL, 'p' },
{"taxid", required_argument, NULL, 'x' },
{"comp_based_stats", required_argument, NULL, 'C' },
{"query_gencode", required_argument, NULL, 'Q' },
{"db_gencode", required_argument, NULL, 'D' },
{"filter", required_argument, NULL, 'F' },
{"subalignments", required_argument, NULL, 'K' },
{"dump", required_argument, NULL, 'N' },
{"out", required_argument, NULL, 'o' },
{"dbsize", required_argument, NULL, 'z' },
{"show_gis", no_argument, NULL, 'I' },
{"show_taxid", no_argument, NULL, 'H' },
{"help", no_argument, NULL, 'h' },
{ 0, 0, 0, 0 }
};
int option_index = 0;
int c;
while (1)
{
c = getopt_long(argc, argv, short_options, long_options, &option_index);
if (c == -1)
break;
switch(c)
{
case 'a':
/* threads */
threads = atol(optarg);
break;
case 'b':
/* alignments */
alignments = atol(optarg);
break;
case 'c':
/* min score threshold */
minscore = atol(optarg);
break;
case 'C':
/* composition-based adjustments */
if ( (strcasecmp(optarg, "F") != 0) && (strcmp(optarg, "0") != 0) )
fatal("Composition-based score adjustments not supported.");
break;
case 'd':
/* database */
databasename = optarg;
break;
case 'D':
/* database genetic code */
db_gencode = atol(optarg);
break;
case 'e':
/* evalue */
expect = atof(optarg);
break;
case 'E':
/* gap extend */
gapextend = atol(optarg);
break;
case 'F':
/* filter */
if ( (strlen(optarg) != 0) && (strcasecmp(optarg, "F") != 0) )
fatal("Query sequence filtering not supported.");
break;
case 'G':
/* gap open */
gapopen = atol(optarg);
break;
case 'h':
args_help();
exit(1);
break;
case 'H':
/* show_taxid */
show_taxid = 1;
break;
case 'i':
/* query */
queryname = optarg;
break;
case 'I':
/* show_gis */
show_gis = 1;
break;
case 'k':
/* min evalue threshold */
minexpect = atof(optarg);
break;
case 'K':
/* subalignments */
subalignments = atol(optarg);
break;
case 'm':
/* view */
view = atol(optarg);
break;
case 'M':
/* matrix */
matrixname = optarg;
break;
case 'N':
/* dump */
dump = atol(optarg);