static void
process_SearchCmd(HMMD_COMMAND *cmd, WORKER_ENV *env)
{
int i;
int cnt;
int limit;
int status;
int blk_size;
WORKER_INFO *info = NULL;
ESL_ALPHABET *abc;
ESL_STOPWATCH *w;
ESL_THREADS *threadObj = NULL;
pthread_mutex_t inx_mutex;
int current_index;
QUEUE_DATA *query = NULL;
time_t date;
char timestamp[32];
w = esl_stopwatch_Create();
abc = esl_alphabet_Create(eslAMINO);
if (pthread_mutex_init(&inx_mutex, NULL) != 0) p7_Fail("mutex init failed");
ESL_ALLOC(info, sizeof(*info) * env->ncpus);
/* Log the current time (at search start) */
date = time(NULL);
ctime_r(&date, timestamp);
printf("\n%s", timestamp); /* note that ctime_r() leaves \n on end of timestamp */
/* initialize thread data */
query = process_QueryCmd(cmd, env);
esl_stopwatch_Start(w);
info->range_list = NULL;
if (esl_opt_IsUsed(query->opts, "--seqdb_ranges")) {
ESL_ALLOC(info->range_list, sizeof(RANGE_LIST));
hmmpgmd_GetRanges(info->range_list, esl_opt_GetString(query->opts, "--seqdb_ranges"));
}
if (query->cmd_type == HMMD_CMD_SEARCH) threadObj = esl_threads_Create(&search_thread);
else threadObj = esl_threads_Create(&scan_thread);
if (query->query_type == HMMD_SEQUENCE) {
fprintf(stdout, "Search seq %s [L=%ld]", query->seq->name, (long) query->seq->n);
} else {
fprintf(stdout, "Search hmm %s [M=%d]", query->hmm->name, query->hmm->M);
}
fprintf(stdout, " vs %s DB %d [%d - %d]",
(query->cmd_type == HMMD_CMD_SEARCH) ? "SEQ" : "HMM",
query->dbx, query->inx, query->inx + query->cnt - 1);
if (info->range_list)
fprintf(stdout, " in range(s) %s", esl_opt_GetString(query->opts, "--seqdb_ranges"));
fprintf(stdout, "\n");
/* Create processing pipeline and hit list */
for (i = 0; i < env->ncpus; ++i) {
info[i].abc = query->abc;
info[i].hmm = query->hmm;
info[i].seq = query->seq;
info[i].opts = query->opts;
info[i].range_list = info[0].range_list;
info[i].th = NULL;
info[i].pli = NULL;
info[i].inx_mutex = &inx_mutex;
info[i].inx = ¤t_index;/* this is confusing trickery - to share a single variable across all threads */
info[i].blk_size = &blk_size; /* ditto */
info[i].limit = &limit; /* ditto. TODO: come back and clean this up. */
if (query->cmd_type == HMMD_CMD_SEARCH) {
HMMER_SEQ **list = env->seq_db->db[query->dbx].list;
info[i].sq_list = &list[query->inx];
info[i].sq_cnt = query->cnt;
info[i].db_Z = env->seq_db->db[query->dbx].K;
info[i].om_list = NULL;
info[i].om_cnt = 0;
} else {
info[i].sq_list = NULL;
info[i].sq_cnt = 0;
info[i].db_Z = 0;
info[i].om_list = &env->hmm_db->list[query->inx];
info[i].om_cnt = query->cnt;
}
esl_threads_AddThread(threadObj, &info[i]);
}
/* try block size of 5000. we will need enough sequences for four
* blocks per thread or better.
*/
blk_size = 5000;
cnt = query->cnt / env->ncpus / blk_size;
limit = query->cnt * 2 / 3;
if (cnt < 4) {
/* try block size of 1000 */
blk_size /= 5;
cnt = query->cnt / env->ncpus / blk_size;
if (cnt < 4) {
/* still not enough. just divide it up into one block per thread */
blk_size = query->cnt / env->ncpus + 1;
limit = query->cnt * 2;
}
}
current_index = 0;
esl_threads_WaitForStart(threadObj);
esl_threads_WaitForFinish(threadObj);
esl_stopwatch_Stop(w);
#if 1
fprintf (stdout, " Sequences Residues Elapsed\n");
for (i = 0; i < env->ncpus; ++i) {
print_timings(i, info[i].elapsed, info[i].pli);
}
#endif
/* merge the results of the search results */
for (i = 1; i < env->ncpus; ++i) {
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
}
print_timings(99, w->elapsed, info[0].pli);
send_results(env->fd, w, info);
/* free the last of the pipeline data */
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
free_QueueData(query);
esl_threads_Destroy(threadObj);
pthread_mutex_destroy(&inx_mutex);
if (info->range_list) {
if (info->range_list->starts) free(info->range_list->starts);
if (info->range_list->ends) free(info->range_list->ends);
free (info->range_list);
}
free(info);
esl_stopwatch_Destroy(w);
esl_alphabet_Destroy(abc);
return;
ERROR:
LOG_FATAL_MSG("malloc", errno);
}
int
main(void)
{
int i;
int ncpu = 4;
int iter = 25;
WORK_INFO *worker = NULL;
ESL_THREADS *thr = NULL;
ESL_WORK_QUEUE *queue = NULL;
int *objs = NULL;
int *obj;
objs = malloc(sizeof(int) * ncpu * 2);
worker = malloc(sizeof(WORK_INFO) * ncpu);
thr = esl_threads_Create(&worker_thread);
/* Create a work queue that is able to hold two items per thread.
* The idea is that while one object is being processed by a
* worker thread, another item is being readied. So, when the
* worker thread has completed processing its current object,
* its next object to processes is hopefully waiting.
*/
queue = esl_workqueue_Create(ncpu * 2);
for (i = 0; i < ncpu * 2; i++)
{
objs[i] = 0;
esl_workqueue_Init(queue, &objs[i]);
}
for (i = 0; i < ncpu; i++)
{
worker[i].id = 'A' + i;
worker[i].queue = queue;
esl_threads_AddThread(thr, (void *) &worker[i]);
}
esl_threads_WaitForStart (thr);
/* For N number of iterations, get an object that has been
* processed, i.e. on the readers input queue and place it
* on the ready queue.
*/
esl_workqueue_ReaderUpdate(queue, NULL, (void **) &obj);
for (i = 1; i <= iter; ++i)
{
*obj = i;
printf("Item %d is ready to be processed\n", *obj);
esl_workqueue_ReaderUpdate(queue, obj, (void **) &obj);
}
/* put zeros on the queues to signal the worker that we are done */
for (i = 0; i < ncpu; ++i)
{
*obj = 0;
esl_workqueue_ReaderUpdate(queue, obj, (void **) &obj);
}
/* The worker threads now run their work. */
esl_threads_WaitForFinish(thr);
esl_threads_Destroy(thr);
esl_workqueue_Destroy(queue);
free(worker);
free(objs);
return eslOK;
}
/* serial_master()
* The serial version of hmmbuild.
* For each MSA, build an HMM and save it.
*
* A master can only return if it's successful. All errors are handled immediately and fatally with p7_Fail().
*/
static int
serial_master(const ESL_GETOPTS *go, struct cfg_s *cfg)
{
int status;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
WORK_ITEM *item = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errmsg[eslERRBUFSIZE];
if ((status = init_master_cfg(go, cfg, errmsg)) != eslOK) p7_Fail(errmsg);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(cfg->abc);
info[i].bld = p7_builder_Create(go, cfg->abc);
if (info[i].bld == NULL) p7_Fail("p7_builder_Create failed");
#ifdef HMMER_THREADS
info[i].queue = queue;
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
ESL_ALLOC(item, sizeof(*item));
item->nali = 0;
item->processed = FALSE;
item->postmsa = NULL;
item->msa = NULL;
item->hmm = NULL;
item->entropy = 0.0;
status = esl_workqueue_Init(queue, item);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
#ifdef HMMER_THREADS
if (ncpus > 0) status = thread_loop(threadObj, queue, cfg);
else status = serial_loop(info, cfg);
#else
status = serial_loop(info, cfg);
#endif
if (status == eslEFORMAT) esl_fatal("Alignment file parse error:\n%s\n", cfg->afp->errbuf);
else if (status == eslEINVAL) esl_fatal("Alignment file parse error:\n%s\n", cfg->afp->errbuf);
else if (status != eslEOF) esl_fatal("Alignment file read failed with error code %d\n", status);
for (i = 0; i < infocnt; ++i)
{
p7_bg_Destroy(info[i].bg);
p7_builder_Destroy(info[i].bld);
}
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &item) == eslOK)
{
free(item);
}
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
return eslOK;
ERROR:
return eslFAIL;
}
/* serial_master()
* The serial version of hmmsearch.
* For each query HMM in <hmmdb> search the database for hits.
*
* A master can only return if it's successful. All errors are handled
* immediately and fatally with p7_Fail().
*/
static int
serial_master(ESL_GETOPTS *go, struct cfg_s *cfg)
{
FILE *ofp = stdout; /* output file for results (default stdout) */
FILE *tblfp = NULL; /* output stream for tabular per-seq (--tblout) */
FILE *dfamtblfp = NULL; /* output stream for tabular Dfam format (--dfamtblout) */
FILE *aliscoresfp = NULL; /* output stream for alignment scores (--aliscoresout) */
// P7_HMM *hmm = NULL; /* one HMM query */
// P7_SCOREDATA *scoredata = NULL;
int seqfmt = eslSQFILE_UNKNOWN; /* format of seqfile */
ESL_SQFILE *sqfp = NULL; /* open seqfile */
P7_HMMFILE *hfp = NULL; /* open HMM database file */
ESL_ALPHABET *abc = NULL; /* sequence alphabet */
P7_OPROFILE *om = NULL; /* target profile */
ESL_STOPWATCH *w = NULL; /* timing */
ESL_SQ *qsq = NULL; /* query sequence */
int nquery = 0;
int textw;
int status = eslOK;
int hstatus = eslOK;
int sstatus = eslOK;
int i;
int ncpus = 0;
int infocnt = 0;
WORKER_INFO *info = NULL;
#ifdef HMMER_THREADS
P7_OM_BLOCK *block = NULL;
ESL_THREADS *threadObj= NULL;
ESL_WORK_QUEUE *queue = NULL;
#endif
char errbuf[eslERRBUFSIZE];
double window_beta = -1.0 ;
int window_length = -1;
if (esl_opt_IsUsed(go, "--w_beta")) { if ( ( window_beta = esl_opt_GetReal(go, "--w_beta") ) < 0 || window_beta > 1 ) esl_fatal("Invalid window-length beta value\n"); }
if (esl_opt_IsUsed(go, "--w_length")) { if (( window_length = esl_opt_GetInteger(go, "--w_length")) < 4 ) esl_fatal("Invalid window length value\n"); }
w = esl_stopwatch_Create();
if (esl_opt_GetBoolean(go, "--notextw")) textw = 0;
else textw = esl_opt_GetInteger(go, "--textw");
/* If caller declared an input format, decode it */
if (esl_opt_IsOn(go, "--qformat")) {
seqfmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--qformat"));
if (seqfmt == eslSQFILE_UNKNOWN) p7_Fail("%s is not a recognized input sequence file format\n", esl_opt_GetString(go, "--qformat"));
}
/* validate options if running as a daemon */
// if (esl_opt_IsOn(go, "--daemon")) {
/* running as a daemon, the input format must be type daemon */
// if (seqfmt != eslSQFILE_UNKNOWN && seqfmt != eslSQFILE_DAEMON)
// esl_fatal("Input format %s not supported. Must be daemon\n", esl_opt_GetString(go, "--qformat"));
// seqfmt = eslSQFILE_DAEMON;
// if (strcmp(cfg->seqfile, "-") != 0) esl_fatal("Query sequence file must be '-'\n");
// }
/* Open the target profile database to get the sequence alphabet */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, errbuf);
if (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status == eslEFORMAT) p7_Fail("File format problem, trying to open HMM file %s.\n%s\n", cfg->hmmfile, errbuf);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n", status, cfg->hmmfile, errbuf);
if (! hfp->is_pressed) p7_Fail("Failed to open binary auxfiles for %s: use hmmpress first\n", hfp->fname);
hstatus = p7_oprofile_ReadMSV(hfp, &abc, &om);
if (hstatus == eslEFORMAT) p7_Fail("bad format, binary auxfiles, %s:\n%s", cfg->hmmfile, hfp->errbuf);
else if (hstatus == eslEINCOMPAT) p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile);
else if (hstatus != eslOK) p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
p7_oprofile_Destroy(om);
p7_hmmfile_Close(hfp);
/* Open the query sequence database */
status = esl_sqfile_OpenDigital(abc, cfg->seqfile, seqfmt, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open sequence file %s for reading\n", cfg->seqfile);
else if (status == eslEFORMAT) p7_Fail("Sequence file %s is empty or misformatted\n", cfg->seqfile);
else if (status == eslEINVAL) p7_Fail("Can't autodetect format of a stdin or .gz seqfile");
else if (status != eslOK) p7_Fail("Unexpected error %d opening sequence file %s\n", status, cfg->seqfile);
if (sqfp->format > 100) // breaking the law! That range is reserved for msa, for aligned formats
p7_Fail("%s contains a multiple sequence alignment; expect unaligned sequences, like FASTA\n", cfg->seqfile);
qsq = esl_sq_CreateDigital(abc);
/* Open the results output files */
if (esl_opt_IsOn(go, "-o")) { if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL) esl_fatal("Failed to open output file %s for writing\n", esl_opt_GetString(go, "-o")); }
if (esl_opt_IsOn(go, "--tblout")) { if ((tblfp = fopen(esl_opt_GetString(go, "--tblout"), "w")) == NULL) esl_fatal("Failed to open tabular per-seq output file %s for writing\n", esl_opt_GetString(go, "--tblfp")); }
if (esl_opt_IsOn(go, "--dfamtblout")) { if ((dfamtblfp = fopen(esl_opt_GetString(go, "--dfamtblout"),"w")) == NULL) esl_fatal("Failed to open tabular dfam output file %s for writing\n", esl_opt_GetString(go, "--dfamtblout")); }
if (esl_opt_IsOn(go, "--aliscoresout")) { if ((aliscoresfp = fopen(esl_opt_GetString(go, "--aliscoresout"),"w")) == NULL) esl_fatal("Failed to open alignment scores output file %s for writing\n", esl_opt_GetString(go, "--aliscoresout")); }
output_header(ofp, go, cfg->hmmfile, cfg->seqfile);
#ifdef HMMER_THREADS
/* initialize thread data */
if (esl_opt_IsOn(go, "--cpu")) ncpus = esl_opt_GetInteger(go, "--cpu");
else esl_threads_CPUCount(&ncpus);
if (ncpus > 0)
{
threadObj = esl_threads_Create(&pipeline_thread);
queue = esl_workqueue_Create(ncpus * 2);
}
#endif
infocnt = (ncpus == 0) ? 1 : ncpus;
ESL_ALLOC(info, sizeof(*info) * infocnt);
for (i = 0; i < infocnt; ++i)
{
info[i].bg = p7_bg_Create(abc);
#ifdef HMMER_THREADS
info[i].queue = queue;
#endif
}
#ifdef HMMER_THREADS
for (i = 0; i < ncpus * 2; ++i)
{
block = p7_oprofile_CreateBlock(BLOCK_SIZE);
if (block == NULL) esl_fatal("Failed to allocate sequence block");
status = esl_workqueue_Init(queue, block);
if (status != eslOK) esl_fatal("Failed to add block to work queue");
}
#endif
/* Outside loop: over each query sequence in <seqfile>. */
while ((sstatus = esl_sqio_Read(sqfp, qsq)) == eslOK)
{
if (sstatus == eslEMEM) p7_Fail("Memory allocation error reading sequence file\n", status);
if (sstatus == eslEINCONCEIVABLE) p7_Fail("Unexpected error %d reading sequence file\n", status);
// if (qsq->L > NHMMER_MAX_RESIDUE_COUNT) p7_Fail("Input sequence %s in file %s exceeds maximum length of %d bases.\n", qsq->name, cfg->seqfile, NHMMER_MAX_RESIDUE_COUNT);
nquery++;
esl_stopwatch_Start(w);
/* Open the target profile database */
status = p7_hmmfile_OpenE(cfg->hmmfile, p7_HMMDBENV, &hfp, NULL);
if (status != eslOK) p7_Fail("Unexpected error %d in opening hmm file %s.\n", status, cfg->hmmfile);
#ifdef HMMER_THREADS
/* if we are threaded, create a lock to prevent multiple readers */
if (ncpus > 0)
{
status = p7_hmmfile_CreateLock(hfp);
if (status != eslOK) p7_Fail("Unexpected error %d creating lock\n", status);
}
#endif
if (fprintf(ofp, "Query: %s [L=%ld]\n", qsq->name, (long) qsq->n) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->acc[0] != 0 && fprintf(ofp, "Accession: %s\n", qsq->acc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (qsq->desc[0] != 0 && fprintf(ofp, "Description: %s\n", qsq->desc) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
for (i = 0; i < infocnt; ++i)
{
/* Create processing pipeline and hit list */
info[i].th = p7_tophits_Create();
info[i].pli = p7_pipeline_Create(go, 100, 100, TRUE, p7_SCAN_MODELS); /* M_hint = 100, L_hint = 100 are just dummies for now */
info[i].pli->hfp = hfp; /* for two-stage input, pipeline needs <hfp> */
p7_pli_NewSeq(info[i].pli, qsq);
info[i].qsq = qsq;
if ( esl_opt_IsUsed(go, "--toponly") )
info[i].pli->strand = p7_STRAND_TOPONLY;
else if ( esl_opt_IsUsed(go, "--bottomonly") )
info[i].pli->strand = p7_STRAND_BOTTOMONLY;
else
info[i].pli->strand = p7_STRAND_BOTH;
#ifdef HMMER_THREADS
if (ncpus > 0) esl_threads_AddThread(threadObj, &info[i]);
#endif
}
#ifdef HMMER_THREADS
if (ncpus > 0) hstatus = thread_loop(threadObj, queue, hfp);
else hstatus = serial_loop(info, hfp);
#else
hstatus = serial_loop(info, hfp);
#endif
switch(hstatus)
{
case eslEFORMAT: p7_Fail("bad file format in HMM file %s", cfg->hmmfile); break;
case eslEINCOMPAT: p7_Fail("HMM file %s contains different alphabets", cfg->hmmfile); break;
case eslEOF:
case eslOK: /* do nothing */
break;
default: p7_Fail("Unexpected error in reading HMMs from %s", cfg->hmmfile);
}
/* merge the results of the search results */
for (i = 1; i < infocnt; ++i)
{
p7_tophits_Merge(info[0].th, info[i].th);
p7_pipeline_Merge(info[0].pli, info[i].pli);
p7_pipeline_Destroy(info[i].pli);
p7_tophits_Destroy(info[i].th);
}
/* modify e-value to account for number of models */
for (i = 0; i < info->th->N ; i++)
{
info->th->unsrt[i].lnP += log((float)info->pli->nmodels);
info->th->unsrt[i].dcl[0].lnP = info->th->unsrt[i].lnP;
info->th->unsrt[i].sortkey = -1.0 * info->th->unsrt[i].lnP;
}
/* it's possible to have duplicates based on how viterbi ranges can overlap */
p7_tophits_SortByModelnameAndAlipos(info->th);
p7_tophits_RemoveDuplicates(info->th, info->pli->use_bit_cutoffs);
/* Print results */
p7_tophits_SortBySortkey(info->th);
p7_tophits_Threshold(info->th, info->pli);
//tally up total number of hits and target coverage
info->pli->n_output = info->pli->pos_output = 0;
for (i = 0; i < info->th->N; i++) {
if ( (info->th->hit[i]->flags & p7_IS_REPORTED) || info->th->hit[i]->flags & p7_IS_INCLUDED) {
info->pli->n_output++;
info->pli->pos_output += abs(info->th->hit[i]->dcl[0].jali - info->th->hit[i]->dcl[0].iali) + 1;
}
}
p7_tophits_Targets(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
p7_tophits_Domains(ofp, info->th, info->pli, textw); if (fprintf(ofp, "\n\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
if (tblfp) p7_tophits_TabularTargets(tblfp, qsq->name, qsq->acc, info->th, info->pli, (nquery == 1));
if (dfamtblfp) p7_tophits_TabularXfam(dfamtblfp, qsq->name, NULL, info->th, info->pli);
if (aliscoresfp) p7_tophits_AliScores(aliscoresfp, qsq->name, info->th );
esl_stopwatch_Stop(w);
info->pli->nseqs = 1;
p7_pli_Statistics(ofp, info->pli, w);
if (fprintf(ofp, "//\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
fflush(ofp);
p7_hmmfile_Close(hfp);
p7_pipeline_Destroy(info->pli);
p7_tophits_Destroy(info->th);
esl_sq_Reuse(qsq);
}
if (sstatus == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (sstatus != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
sstatus, sqfp->filename);
/* Terminate outputs - any last words?
*/
if (tblfp) p7_tophits_TabularTail(tblfp, "hmmscan", p7_SCAN_MODELS, cfg->seqfile, cfg->hmmfile, go);
if (ofp) { if (fprintf(ofp, "[ok]\n") < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed"); }
/* Cleanup - prepare for successful exit
*/
for (i = 0; i < infocnt; ++i)
p7_bg_Destroy(info[i].bg);
#ifdef HMMER_THREADS
if (ncpus > 0)
{
esl_workqueue_Reset(queue);
while (esl_workqueue_Remove(queue, (void **) &block) == eslOK)
p7_oprofile_DestroyBlock(block);
esl_workqueue_Destroy(queue);
esl_threads_Destroy(threadObj);
}
#endif
free(info);
esl_sq_Destroy(qsq);
esl_stopwatch_Destroy(w);
esl_alphabet_Destroy(abc);
esl_sqfile_Close(sqfp);
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return eslOK;
ERROR:
if (ofp != stdout) fclose(ofp);
if (tblfp) fclose(tblfp);
if (dfamtblfp) fclose(dfamtblfp);
if (aliscoresfp) fclose(aliscoresfp);
return status;
}
