void gt_querymatchoutoptions_delete(
GtQuerymatchoutoptions *querymatchoutoptions)
{
if (querymatchoutoptions != NULL)
{
front_trace_delete(querymatchoutoptions->front_trace);
gt_greedy_extend_matchinfo_delete(querymatchoutoptions->ggemi);
gt_free(querymatchoutoptions);
}
}
static int gt_seed_extend_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
GtSeedExtendArguments *arguments = tool_arguments;
GtEncseqLoader *encseq_loader = NULL;
GtEncseq *aencseq = NULL, *bencseq = NULL;
GtGreedyextendmatchinfo *grextinfo = NULL;
GtXdropmatchinfo *xdropinfo = NULL;
GtQuerymatchoutoptions *querymatchoutopt = NULL;
GtTimer *seedextendtimer = NULL;
GtExtendCharAccess cam = GT_EXTEND_CHAR_ACCESS_ANY;
GtUword errorpercentage = 0UL;
int had_err = 0;
gt_error_check(err);
gt_assert(arguments != NULL);
gt_assert(arguments->se_minidentity >= GT_EXTEND_MIN_IDENTITY_PERCENTAGE &&
arguments->se_minidentity <= 100UL);
/* Calculate error percentage from minidentity */
errorpercentage = 100UL - arguments->se_minidentity;
/* Measure whole running time */
if (arguments->benchmark || arguments->verbose) {
gt_showtime_enable();
}
if (gt_showtime_enabled())
{
seedextendtimer = gt_timer_new();
gt_timer_start(seedextendtimer);
}
/* Load encseq A */
encseq_loader = gt_encseq_loader_new();
gt_encseq_loader_enable_autosupport(encseq_loader);
aencseq = gt_encseq_loader_load(encseq_loader,
gt_str_get(arguments->dbs_indexname),
err);
if (aencseq == NULL)
had_err = -1;
/* If there is a 2nd read set: Load encseq B */
if (!had_err) {
if (strcmp(gt_str_get(arguments->dbs_queryname), "") != 0) {
bencseq = gt_encseq_loader_load(encseq_loader,
gt_str_get(arguments->dbs_queryname),
err);
} else {
bencseq = gt_encseq_ref(aencseq);
}
if (bencseq == NULL) {
had_err = -1;
gt_encseq_delete(aencseq);
}
}
gt_encseq_loader_delete(encseq_loader);
/* set character access method */
if (!had_err && (gt_option_is_set(arguments->se_option_greedy) ||
gt_option_is_set(arguments->se_option_xdrop) ||
arguments->se_alignmentwidth > 0))
{
cam = gt_greedy_extend_char_access(gt_str_get
(arguments->se_char_access_mode),
err);
if ((int) cam == -1) {
had_err = -1;
gt_encseq_delete(aencseq);
gt_encseq_delete(bencseq);
}
}
/* Use bias dependent parameters, adapted from E. Myers' DALIGNER */
if (!had_err && arguments->bias_parameters) {
const GtAlphabet *alpha = gt_encseq_alphabet(aencseq);
const double bias_factor[10] = {.690, .690, .690, .690, .780,
.850, .900, .933, .966, 1.000};
if (gt_alphabet_is_dna(alpha)) {
GtUword at, cg;
at = gt_encseq_charcount(aencseq, gt_alphabet_encode(alpha, 'a'));
at += gt_encseq_charcount(aencseq, gt_alphabet_encode(alpha, 't'));
cg = gt_encseq_charcount(aencseq, gt_alphabet_encode(alpha, 'c'));
cg += gt_encseq_charcount(aencseq, gt_alphabet_encode(alpha, 'g'));
if (at + cg > 0) {
const double ratio = (double)MIN(at, cg) / (at + cg);
int bias_index = (int)MAX(0.0, (ratio + 0.025) * 20.0 - 1.0);
gt_assert(bias_index < 10);
arguments->se_maxalilendiff = 30;
arguments->se_perc_match_hist = (GtUword)(100.0 - errorpercentage *
bias_factor[bias_index]);
if (arguments->verbose) {
printf("# Base ratio = %4.2lf -> percmathistory = "GT_WU"\n",
ratio, arguments->se_perc_match_hist);
}
} else {
had_err = -1;
}
} else {
had_err = -1;
}
if (had_err) {
gt_error_set(err, "option \"-bias-parameters\" can only be applied to "
"the DNA alphabet");
gt_encseq_delete(aencseq);
gt_encseq_delete(bencseq);
}
}
/* Prepare options for greedy extension */
if (!had_err && gt_option_is_set(arguments->se_option_greedy)) {
grextinfo = gt_greedy_extend_matchinfo_new(errorpercentage,
arguments->se_maxalilendiff,
arguments->se_historysize,
arguments->se_perc_match_hist,
arguments->se_alignlength,
cam,
arguments->se_extendgreedy);
if (arguments->benchmark) {
gt_greedy_extend_matchinfo_silent_set(grextinfo);
}
}
/* Prepare options for xdrop extension */
if (!had_err && gt_option_is_set(arguments->se_option_xdrop)) {
xdropinfo = gt_xdrop_matchinfo_new(arguments->se_alignlength,
errorpercentage,
arguments->se_xdropbelowscore,
arguments->se_extendxdrop);
if (arguments->benchmark) {
gt_xdrop_matchinfo_silent_set(xdropinfo);
}
}
/* Prepare output options */
if (!had_err && (arguments->se_alignmentwidth > 0 ||
gt_option_is_set(arguments->se_option_xdrop)))
{
querymatchoutopt
= gt_querymatchoutoptions_new(arguments->se_alignmentwidth);
if (gt_option_is_set(arguments->se_option_xdrop) ||
gt_option_is_set(arguments->se_option_greedy))
{
const GtUword sensitivity = gt_option_is_set(arguments->se_option_greedy)
? arguments->se_extendgreedy : 100;
gt_querymatchoutoptions_extend(querymatchoutopt,
errorpercentage,
arguments->se_maxalilendiff,
arguments->se_historysize,
arguments->se_perc_match_hist,
cam,
sensitivity);
}
}
/* Start algorithm */
if (!had_err) {
GtDiagbandseed dbsarguments;
dbsarguments.errorpercentage = errorpercentage;
dbsarguments.userdefinedleastlength = arguments->se_alignlength;
dbsarguments.seedlength = arguments->dbs_seedlength;
dbsarguments.logdiagbandwidth = arguments->dbs_logdiagbandwidth;
dbsarguments.mincoverage = arguments->dbs_mincoverage;
dbsarguments.maxfreq = arguments->dbs_maxfreq;
dbsarguments.memlimit = arguments->dbs_memlimit;
dbsarguments.mirror = arguments->mirror;
dbsarguments.overlappingseeds = arguments->overlappingseeds;
dbsarguments.verify = arguments->dbs_verify;
dbsarguments.verbose = arguments->verbose;
dbsarguments.debug_kmer = arguments->dbs_debug_kmer;
dbsarguments.debug_seedpair = arguments->dbs_debug_seedpair;
dbsarguments.seed_display = arguments->seed_display;
dbsarguments.extendgreedyinfo = grextinfo;
dbsarguments.extendxdropinfo = xdropinfo;
dbsarguments.querymatchoutopt = querymatchoutopt;
had_err = gt_diagbandseed_run(aencseq, bencseq, &dbsarguments, err);
/* clean up */
gt_encseq_delete(aencseq);
gt_encseq_delete(bencseq);
if (gt_option_is_set(arguments->se_option_greedy)) {
gt_greedy_extend_matchinfo_delete(grextinfo);
}
if (gt_option_is_set(arguments->se_option_xdrop)) {
gt_xdrop_matchinfo_delete(xdropinfo);
}
if (arguments->se_alignmentwidth > 0 ||
gt_option_is_set(arguments->se_option_xdrop)) {
gt_querymatchoutoptions_delete(querymatchoutopt);
}
}
if (gt_showtime_enabled()) {
if (!had_err) {
char *keystring
= gt_seed_extend_params_keystring(gt_option_is_set(arguments->
se_option_greedy),
gt_option_is_set(arguments->
se_option_xdrop),
arguments->dbs_seedlength,
arguments->se_alignlength,
arguments->se_minidentity,
arguments->se_maxalilendiff,
arguments->se_perc_match_hist,
arguments->se_extendgreedy,
arguments->se_extendxdrop,
arguments->se_xdropbelowscore);
printf("# TIME seedextend-%s", keystring);
gt_free(keystring);
gt_timer_show_formatted(seedextendtimer,
" overall " GT_WD ".%06ld\n",
stdout);
}
gt_timer_delete(seedextendtimer);
}
return had_err;
}
static int gt_show_seedext_runner(GT_UNUSED int argc,
GT_UNUSED const char **argv,
GT_UNUSED int parsed_args,
void *tool_arguments,
GtError *err)
{
int had_err = 0;
GtUword alignmentwidth;
GtShowSeedextArguments *arguments = tool_arguments;
GtSeedextendMatchIterator *semi;
gt_error_check(err);
gt_assert(arguments != NULL);
/* Parse option string in first line of file specified by filename. */
alignmentwidth = arguments->show_alignment ? 70 : 0;
semi = gt_seedextend_match_iterator_new(arguments->matchfilename,err);
if (semi == NULL)
{
had_err = -1;
}
/* Parse seed extensions. */
if (!had_err)
{
const GtEncseq *aencseq = gt_seedextend_match_iterator_aencseq(semi),
*bencseq = gt_seedextend_match_iterator_bencseq(semi);
GtAlignment *alignment = gt_alignment_new();
Polishing_info *pol_info = NULL;
GtSequencepairbuffer seqpairbuf = {NULL,NULL,0,0};
/* the following are used if seed_extend is set */
GtGreedyextendmatchinfo *greedyextendmatchinfo = NULL;
GtProcessinfo_and_querymatchspaceptr processinfo_and_querymatchspaceptr;
const GtUchar *characters = gt_encseq_alphabetcharacters(aencseq);
const GtUchar wildcardshow = gt_encseq_alphabetwildcardshow(aencseq);
GtUchar *alignment_show_buffer
= arguments->show_alignment ? gt_alignment_buffer_new(alignmentwidth)
: NULL;
GtLinspaceManagement *linspace_spacemanager = gt_linspaceManagement_new();
GtScoreHandler *linspace_scorehandler = gt_scorehandler_new(0,1,0,1);;
if (!arguments->relax_polish)
{
double matchscore_bias = GT_DEFAULT_MATCHSCORE_BIAS;
if (gt_seedextend_match_iterator_bias_parameters(semi))
{
matchscore_bias = gt_greedy_dna_sequence_bias_get(aencseq);
}
pol_info = polishing_info_new_with_bias(
gt_seedextend_match_iterator_errorpercentage(semi),
matchscore_bias,
gt_seedextend_match_iterator_history_size(semi));
}
if (arguments->seed_display)
{
gt_seedextend_match_iterator_seed_display_set(semi);
}
if (arguments->show_alignment || arguments->showeoplist)
{
gt_seedextend_match_iterator_querymatchoutoptions_set(semi,
true,
arguments->showeoplist,
alignmentwidth,
!arguments->relax_polish,
arguments->seed_display);
}
if (arguments->seed_extend)
{
greedyextendmatchinfo
= gt_greedy_extend_matchinfo_new(70,
GT_MAX_ALI_LEN_DIFF,
gt_seedextend_match_iterator_history_size(semi),
GT_MIN_PERC_MAT_HISTORY,
0, /* userdefinedleastlength */
GT_EXTEND_CHAR_ACCESS_ANY,
100,
pol_info);
}
if (pol_info != NULL)
{
gt_alignment_polished_ends(alignment,pol_info,false);
}
processinfo_and_querymatchspaceptr.processinfo = greedyextendmatchinfo;
if (arguments->sortmatches)
{
(void) gt_seedextend_match_iterator_all_sorted(semi,true);
}
while (true)
{
GtQuerymatch *querymatchptr = gt_seedextend_match_iterator_next(semi);
if (querymatchptr == NULL)
{
break;
}
if (gt_seedextend_match_iterator_has_seedline(semi))
{
if (arguments->seed_extend)
{
if (aencseq == bencseq)
{
const GtUword
seedlen = gt_seedextend_match_iterator_seedlen(semi),
seedpos1 = gt_seedextend_match_iterator_seedpos1(semi),
seedpos2 = gt_seedextend_match_iterator_seedpos2(semi);
processinfo_and_querymatchspaceptr.querymatchspaceptr
= querymatchptr;
had_err = gt_greedy_extend_selfmatch_with_output(
&processinfo_and_querymatchspaceptr,
aencseq,
seedlen,
seedpos1,
seedpos2,
err);
if (had_err)
{
break;
}
} else
{
gt_assert(false);
}
} else
{
const GtUword query_totallength
= gt_encseq_seqlength(bencseq,
gt_querymatch_queryseqnum(querymatchptr));
gt_show_seed_extend_encseq(querymatchptr,
aencseq,
bencseq,
query_totallength);
}
} else
{
gt_show_seed_extend_plain(&seqpairbuf,
linspace_spacemanager,
linspace_scorehandler,
alignment,
alignment_show_buffer,
alignmentwidth,
arguments->showeoplist,
characters,
wildcardshow,
aencseq,
bencseq,
querymatchptr);
}
}
polishing_info_delete(pol_info);
gt_greedy_extend_matchinfo_delete(greedyextendmatchinfo);
gt_free(alignment_show_buffer);
gt_scorehandler_delete(linspace_scorehandler);
gt_linspaceManagement_delete(linspace_spacemanager);
gt_free(seqpairbuf.a_sequence);
gt_free(seqpairbuf.b_sequence);
gt_alignment_delete(alignment);
}
gt_seedextend_match_iterator_delete(semi);
return had_err;
}
