/* Function: FM_window_from_diag()
*
* Synopsis: Create a hit window, with sequence-based coordinates, from a diagonal
* holding FM-based coordinates
*
* Details: The submitted diagonal is in FM-based coordinates. Since a single
* FM index might be the concatenation of many sequences in the
* original, this needs to be converted to coordinates in the
* original sequence space (get sequence ID and positions). A diag
* might span multiple input strings, so it is broken up as
* necessary (usually, only one of these will pan out as a legit
* diagonal, but we'll let the next stage sort that out).
*
* Args: diag - The FM-based diagonal
* fm - Data for the FM-index.
* meta - FM metadata from the config
* windowlist - RETURN: collection of SSV-passing windows, with meta data required for downstream stages.
*
* Returns: <eslOK> on success.
*/
static int
FM_window_from_diag (FM_DIAG *diag, const FM_DATA *fm, const FM_METADATA *meta, P7_HMM_WINDOWLIST *windowlist) {
// if diag->complementarity == p7_NOCOMPLEMENT, these positions are in context of FM->T
// otherwise, they're in context of revcomp(FM->T).
int status;
uint32_t seg_id;
uint64_t seg_pos;
status = fm_getOriginalPosition (fm, meta, 0, diag->length, diag->complementarity, diag->n, &seg_id, &seg_pos);
p7_hmmwindow_new(windowlist, seg_id, seg_pos, diag->n, diag->k+diag->length-1, diag->length, diag->score, diag->complementarity,
meta->seq_data[seg_id].length);
return eslOK;
}
/* Function: main()
* Synopsis: Run set of queries against an FM
* Purpose: Read in a FM and a file of query sequences.
* For each query, find matching FM interval, then collect positions in
* the original text T for the corresponding occurrences. These positions
* are 0-based (so first character is position 0).
*/
int
main(int argc, char *argv[])
{
void* tmp; // used for RALLOC calls
clock_t t1, t2;
struct tms ts1, ts2;
char *fname_fm = NULL;
char *fname_queries = NULL;
FM_HIT *hits = NULL;
char *line = NULL;
int status = eslOK;
int hit_cnt = 0;
int hit_indiv_cnt = 0;
int miss_cnt = 0;
int hit_num = 0;
int hit_num2 = 0;
int hits_size = 0;
int i,j;
int count_only = 0;
FM_INTERVAL interval;
FM_DATA *fmsf = NULL;
FM_DATA *fmsb = NULL;
FILE* fp_fm = NULL;
FILE* fp = NULL;
FILE* out = NULL;
char *outname = NULL;
ESL_GETOPTS *go = NULL; /* command line processing */
FM_CFG *cfg;
FM_METADATA *meta;
ESL_SQ *tmpseq; // used for sequence validation
ESL_ALPHABET *abc = NULL;
//start timer
t1 = times(&ts1);
process_commandline(argc, argv, &go, &fname_fm, &fname_queries);
if (esl_opt_IsOn(go, "--out")) {
outname = esl_opt_GetString(go, "--out");
if ( esl_strcmp ("-", outname) == 0 ) {
out = stdout;
outname = "stdout";
} else {
out = fopen(outname,"w");
}
}
if (esl_opt_IsOn(go, "--count_only"))
count_only = 1;
if((fp_fm = fopen(fname_fm, "rb")) == NULL)
esl_fatal("Cannot open file `%s': ", fname_fm);
fm_configAlloc(&cfg);
cfg->occCallCnt = 0;
meta = cfg->meta;
meta->fp = fp_fm;
fm_readFMmeta( meta);
if (meta->alph_type == fm_DNA) abc = esl_alphabet_Create(eslDNA);
else if (meta->alph_type == fm_AMINO) abc = esl_alphabet_Create(eslAMINO);
tmpseq = esl_sq_CreateDigital(abc);
//read in FM-index blocks
ESL_ALLOC(fmsf, meta->block_count * sizeof(FM_DATA) );
if (!meta->fwd_only)
ESL_ALLOC(fmsb, meta->block_count * sizeof(FM_DATA) );
for (i=0; i<meta->block_count; i++) {
fm_FM_read( fmsf+i,meta, TRUE );
if (!meta->fwd_only) {
fm_FM_read(fmsb+i, meta, FALSE );
fmsb[i].SA = fmsf[i].SA;
fmsb[i].T = fmsf[i].T;
}
}
fclose(fp_fm);
output_header(meta, stdout, go, fname_fm, fname_queries);
/* initialize a few global variables, then call initGlobals
* to do architecture-specific initialization
*/
fm_configInit(cfg, NULL);
fm_alphabetCreate(meta, NULL); // don't override charBits
fp = fopen(fname_queries,"r");
if (fp == NULL)
esl_fatal("Unable to open file %s\n", fname_queries);
ESL_ALLOC(line, FM_MAX_LINE * sizeof(char));
hits_size = 200;
ESL_ALLOC(hits, hits_size * sizeof(FM_HIT));
while(fgets(line, FM_MAX_LINE, fp) ) {
int qlen=0;
while (line[qlen] != '\0' && line[qlen] != '\n') qlen++;
if (line[qlen] == '\n') line[qlen] = '\0';
hit_num = 0;
for (i=0; i<meta->block_count; i++) {
fm_getSARangeReverse(fmsf+i, cfg, line, meta->inv_alph, &interval);
if (interval.lower>=0 && interval.lower <= interval.upper) {
int new_hit_num = interval.upper - interval.lower + 1;
hit_num += new_hit_num;
if (!count_only) {
if (hit_num > hits_size) {
hits_size = 2*hit_num;
ESL_RALLOC(hits, tmp, hits_size * sizeof(FM_HIT));
}
getFMHits(fmsf+i, cfg, &interval, i, hit_num-new_hit_num, qlen, hits, fm_forward);
}
}
/* find reverse hits, using backward search on the forward FM*/
if (!meta->fwd_only) {
fm_getSARangeForward(fmsb+i, cfg, line, meta->inv_alph, &interval);// yes, use the backward fm to produce the equivalent of a forward search on the forward fm
if (interval.lower>=0 && interval.lower <= interval.upper) {
int new_hit_num = interval.upper - interval.lower + 1;
hit_num += new_hit_num;
if (!count_only) {
if (hit_num > hits_size) {
hits_size = 2*hit_num;
ESL_RALLOC(hits, tmp, hits_size * sizeof(FM_HIT));
}
//even though I used fmsb above, use fmsf here, since we'll now do a backward trace
//in the FM-index to find the next sampled SA position
getFMHits(fmsf+i, cfg, &interval, i, hit_num-new_hit_num, qlen, hits, fm_backward);
}
}
}
}
if (hit_num > 0) {
if (count_only) {
hit_cnt++;
hit_indiv_cnt += hit_num;
} else {
hit_num2 = 0;
//for each hit, identify the sequence id and position within that sequence
for (i = 0; i< hit_num; i++) {
status = fm_getOriginalPosition (fmsf, meta, hits[i].block, hits[i].length, fm_forward, hits[i].start, &(hits[i].block), &(hits[i].start) );
hits[i].sortkey = (status==eslERANGE ? -1 : meta->seq_data[ hits[i].block ].target_id);
//validate match - if any characters in orig sequence were ambiguities, reject
fm_convertRange2DSQ( fmsf, meta, hits[i].start, hits[i].length, p7_NOCOMPLEMENT, tmpseq, TRUE );
for (j=1; j<=hits[i].length; j++) {
if (tmpseq->dsq[j] >= abc->K) {
hits[i].sortkey = -1; //reject
j = hits[i].length+1; //quit looking
}
}
if (hits[i].sortkey != -1)
hit_num2++; // legitimate hit
}
if (hit_num2 > 0)
hit_cnt++;
//now sort according the the sequence_id corresponding to that seq_offset
qsort(hits, hit_num, sizeof(FM_HIT), hit_sorter);
//skim past the skipped entries
i = 0;
while ( i < hit_num ) {
if (hits[i].sortkey != -1 )
break; //
i++;
}
if (i < hit_num) {
if (out != NULL) {
fprintf (out, "%s\n",line);
//fprintf (out, "\t%10s (%8d %s)\n",meta->seq_data[ hits[i].block ].name, hits[i].start, (hits[i].direction==fm_forward?"+":"-"));
fprintf (out, " %8ld %s %10s\n", (long)(hits[i].start), (hits[i].direction==fm_forward?"f":"r"), meta->seq_data[ hits[i].block ].name);
}
hit_indiv_cnt++;
i++; // skip the first one, since I'll be comparing each to the previous
for ( ; i< hit_num; i++) {
if ( //meta->seq_data[ hits[i].block ].id != meta->seq_data[ hits[i-1].block ].id ||
hits[i].sortkey != hits[i-1].sortkey || //sortkey is seq_data[].id
hits[i].direction != hits[i-1].direction ||
hits[i].start != hits[i-1].start )
{
if (out != NULL)
//fprintf (out, "\t%10s (%8d %s)\n",meta->seq_data[ hits[i].block ].name, hits[i].start, (hits[i].direction==fm_forward?"+":"-"));
fprintf (out, " %8ld %s %10s\n", (long)(hits[i].start), (hits[i].direction==fm_forward?"f":"r"), meta->seq_data[ hits[i].block ].name);
hit_indiv_cnt++;
}
}
if (out != NULL)
fprintf (out, "\n");
}
}
} else {
miss_cnt++;
}
}
for (i=0; i<meta->block_count; i++) {
fm_FM_destroy( fmsf+i, 1 );
if (!meta->fwd_only)
fm_FM_destroy( fmsb+i, 0 );
}
free (hits);
free (line);
fclose(fp);
fm_configDestroy(cfg);
// compute and print the elapsed time in millisec
t2 = times(&ts2);
{
double clk_ticks = sysconf(_SC_CLK_TCK);
double elapsedTime = (t2-t1)/clk_ticks;
double throughput = cfg->occCallCnt/elapsedTime;
fprintf (stderr, "hit: %-10d (%d)\n", hit_cnt, hit_indiv_cnt);
fprintf (stderr, "miss:%-10d\n", miss_cnt);
fprintf (stderr, "run time: %.2f seconds\n", elapsedTime);
fprintf (stderr, "occ calls: %12s\n", commaprint(cfg->occCallCnt));
fprintf (stderr, "occ/sec: %12s\n", commaprint(throughput));
}
exit(eslOK);
ERROR:
printf ("failure allocating memory for hits\n");
exit(status);
}
