/* Print the data for chosen primer pairs to stdout in "boulderio" format. */
void
print_boulder(int io_version,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
int explain_flag) {
/* The pointers to warning tag */
char *warning;
/* A place to put a string containing all error messages */
pr_append_str *combined_retval_err = NULL;
/* A small spacer; WARNING this is a fixed size
buffer, but plenty bigger than
log(2^64, 10), the longest character
string that is needed for a 64 bit integer. */
char suffix [100];
/* Pointers for the primer set just printing */
primer_rec *fwd, *rev, *intl;
/* Variables only used for Primer Lists */
int num_fwd, num_rev, num_int, num_pair, num_print;
int print_fwd = 0;
int print_rev = 0;
int print_int = 0;
/* Switches for printing this primer */
int go_fwd = 0;
int go_rev = 0;
int go_int = 0;
/* The number of loop cycles */
int loop_max;
/* That links to the included region */
int i, incl_s = sa->incl_s;
/* This deals with the renaming of the internal oligo */
const char *new_oligo_name = "INTERNAL";
const char *old_oligo_name = "INTERNAL_OLIGO";
char *int_oligo = (char*) new_oligo_name;
/* Check: are all pointers linked to something*/
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
if (io_version == 3) {
int_oligo = (char*) old_oligo_name;
}
/* Check if there are warnings and print them */
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
printf("PRIMER_WARNING=%s\n", warning);
free(warning);
}
/* Check if a settings file was read an print its id
* Not needed anymore, we do this when we read the setting file. */
/*
if (pa->settings_file_id != NULL) {
printf("P3_FILE_ID=%s\n", pa->settings_file_id);
free(warning);
}
*/
combined_retval_err = create_pr_append_str();
if (NULL == combined_retval_err) exit(-2); /* Out of memory */
if (pr_append_new_chunk_external(combined_retval_err,
retval->glob_err.data))
exit(-2);
if (pr_append_new_chunk_external(combined_retval_err,
retval->per_sequence_err.data))
exit(-2);
/* Check if there are errors, print and return */
if (!pr_is_empty(combined_retval_err)) {
print_boulder_error(pr_append_str_chars(combined_retval_err));
destroy_pr_append_str(combined_retval_err);
return;
}
destroy_pr_append_str(combined_retval_err);
/* Get how many primers are in the array */
num_fwd = retval->fwd.num_elem;
num_rev = retval->rev.num_elem;
num_int = retval->intl.num_elem;
num_pair = retval->best_pairs.num_pairs;
/* Prints out statistics about the primers */
if (explain_flag) print_all_explain(pa, sa, retval, io_version);
/* Print out the stop codon if a reading frame was specified */
if (!PR_START_CODON_POS_IS_NULL(sa))
printf("PRIMER_STOP_CODON_POSITION=%d\n", retval->stop_codon_pos);
/* How often has the loop to be done? */
if (retval->output_type == primer_list) {
/* For Primer Lists: Figure out how many primers are in
* the array that can be printed. If more than needed,
* set it to the number requested. */
/* Get how may primers should be printed */
num_print = pa->num_return;
/* Set how many primers will be printed */
print_fwd = (num_print < num_fwd) ? num_print : num_fwd;
print_rev = (num_print < num_rev) ? num_print : num_rev;
print_int = (num_print < num_int) ? num_print : num_int;
/* Get which list has to print most primers */
loop_max = 0;
if (loop_max < print_fwd) {
loop_max = print_fwd;
}
if (loop_max < print_rev) {
loop_max = print_rev;
}
if (loop_max < print_int) {
loop_max = print_int;
}
/* Now the vars are there how often we have to go
* through the loop and how many of each primer can
* be printed. */
num_pair = 0;
} else {
loop_max = num_pair;
/* Set how many primers will be printed */
print_fwd = num_pair;
print_rev = num_pair;
if (num_int != 0) {
print_int = num_pair;
}
}
if (io_version == 4) {
printf("PRIMER_LEFT_NUM_RETURNED=%d\n", print_fwd);
printf("PRIMER_RIGHT_NUM_RETURNED=%d\n", print_rev);
printf("PRIMER_%s_NUM_RETURNED=%d\n", int_oligo, print_int);
printf("PRIMER_PAIR_NUM_RETURNED=%d\n", num_pair);
}
/* --------------------------------------- */
/* Start of the loop printing all pairs or primers or oligos */
for(i=0; i<loop_max; i++) {
/* What needs to be printed */
/* The conditions for primer lists */
if (retval->output_type == primer_list) {
/* Attach the selected primers to the pointers */
fwd = &retval->fwd.oligo[i];
rev = &retval->rev.oligo[i];
intl = &retval->intl.oligo[i];
/* Do fwd oligos have to be printed? */
if ((pa->pick_left_primer) && (i < print_fwd)) {
go_fwd = 1;
} else {
go_fwd = 0;
}
/* Do rev oligos have to be printed? */
if ((pa->pick_right_primer) && (i < print_rev)) {
go_rev = 1;
} else {
go_rev = 0;
}
/* Do int oligos have to be printed? */
if ((pa->pick_internal_oligo) && (i < print_int)) {
go_int = 1;
} else {
go_int = 0;
}
} else {
/* We will print primer pairs or pairs plus internal oligos */
/* Get pointers to the primer_rec's that we will print */
fwd = retval->best_pairs.pairs[i].left;
rev = retval->best_pairs.pairs[i].right;
intl = retval->best_pairs.pairs[i].intl;
/* Pairs must have fwd and rev primers */
go_fwd = 1;
go_rev = 1;
/* Do hyb oligos have to be printed? */
if (pa->pick_internal_oligo == 1) {
go_int = 1;
} else {
go_int = 0;
}
}
/* Get the number for pimer counting in suffix[0] */
if ((i == 0) && (io_version == 3) ){
suffix[0] = '\0';
} else {
sprintf(suffix, "_%d", i);
}
/* Print out the Pair Penalties */
if (retval->output_type == primer_pairs) {
if (io_version == 3) {
printf("PRIMER_PAIR_PENALTY%s=%.4f\n", suffix,
retval->best_pairs.pairs[i].pair_quality);
} else {
printf("PRIMER_PAIR%s_PENALTY=%f\n", suffix,
retval->best_pairs.pairs[i].pair_quality);
}
}
/* Print single primer penalty */
if (go_fwd == 1)
printf("PRIMER_LEFT%s_PENALTY=%f\n", suffix, fwd->quality);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_PENALTY=%f\n", suffix, rev->quality);
if (go_int == 1)
printf("PRIMER_%s%s_PENALTY=%f\n", int_oligo, suffix, intl->quality);
/* Print the oligo_problems */
if (io_version == 4) {
if (go_fwd == 1 && p3_ol_has_any_problem(fwd))
printf("PRIMER_LEFT%s_PROBLEMS=%s\n", suffix, p3_get_ol_problem_string(fwd));
if (go_rev == 1 && p3_ol_has_any_problem(rev))
printf("PRIMER_RIGHT%s_PROBLEMS=%s\n", suffix, p3_get_ol_problem_string(rev));
if (go_int == 1 && p3_ol_has_any_problem(intl))
printf("PRIMER_%s%s_PROBLEMS=%s\n", int_oligo, suffix, p3_get_ol_problem_string(intl));
}
/* Print primer sequences. */
if (go_fwd == 1)
printf("PRIMER_LEFT%s_SEQUENCE=%s\n", suffix,
pr_oligo_sequence(sa, fwd));
if (go_rev == 1)
printf("PRIMER_RIGHT%s_SEQUENCE=%s\n", suffix,
pr_oligo_rev_c_sequence(sa, rev));
if(go_int == 1)
printf("PRIMER_%s%s_SEQUENCE=%s\n", int_oligo, suffix,
pr_oligo_sequence(sa,intl));
/* Print primer start and length */
if (go_fwd == 1)
printf("PRIMER_LEFT%s=%d,%d\n", suffix,
fwd->start + incl_s + pa->first_base_index,
fwd->length);
if (go_rev == 1)
printf("PRIMER_RIGHT%s=%d,%d\n", suffix,
rev->start + incl_s + pa->first_base_index,
rev->length);
if (go_int == 1)
printf("PRIMER_%s%s=%d,%d\n", int_oligo, suffix,
intl->start + incl_s + pa->first_base_index,
intl->length);
/* Print primer Tm */
if (go_fwd == 1)
printf("PRIMER_LEFT%s_TM=%.3f\n", suffix, fwd->temp);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_TM=%.3f\n", suffix, rev->temp);
if (go_int == 1)
printf("PRIMER_%s%s_TM=%.3f\n", int_oligo, suffix, intl->temp);
/* Print primer GC content */
if (go_fwd == 1)
printf("PRIMER_LEFT%s_GC_PERCENT=%.3f\n", suffix, fwd->gc_content);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_GC_PERCENT=%.3f\n", suffix, rev->gc_content);
if (go_int == 1)
printf("PRIMER_%s%s_GC_PERCENT=%.3f\n", int_oligo, suffix,
intl->gc_content);
/* Print primer self_any */
if (go_fwd == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_LEFT%s_SELF_ANY=%.2f\n", suffix,
fwd->self_any);
if (go_rev == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_RIGHT%s_SELF_ANY=%.2f\n", suffix,
rev->self_any);
if (go_int == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_%s%s_SELF_ANY=%.2f\n", int_oligo, suffix,
intl->self_any);
if (go_int == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_%s%s_SELF_ANY_TH=%.2f\n", int_oligo, suffix,
intl->self_any);
/* Print primer self_any thermodynamical approach */
if (go_fwd == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_LEFT%s_SELF_ANY_TH=%.2f\n", suffix,
fwd->self_any);
if (go_rev == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_RIGHT%s_SELF_ANY_TH=%.2f\n", suffix,
rev->self_any);
/* Print primer self_end*/
if (go_fwd == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_LEFT%s_SELF_END=%.2f\n", suffix,
fwd->self_end);
if (go_rev == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_RIGHT%s_SELF_END=%.2f\n", suffix,
rev->self_end);
if (go_int == 1 && pa->thermodynamic_alignment==0)
printf("PRIMER_%s%s_SELF_END=%.2f\n", int_oligo, suffix,
intl->self_end);
if (go_int == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_%s%s_SELF_END_TH=%.2f\n", int_oligo, suffix,
intl->self_end);
/* Print primer self_end thermodynamical approach */
if (go_fwd == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_LEFT%s_SELF_END_TH=%.2f\n", suffix,
fwd->self_end);
if (go_rev == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_RIGHT%s_SELF_END_TH=%.2f\n", suffix,
rev->self_end);
/* Print primer hairpin */
if (go_fwd == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_LEFT%s_HAIRPIN_TH=%.2f\n", suffix,
fwd->hairpin_th);
if (go_rev == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_RIGHT%s_HAIRPIN_TH=%.2f\n", suffix,
rev->hairpin_th);
if (go_int == 1 && pa->thermodynamic_alignment==1)
printf("PRIMER_%s%s_HAIRPIN_TH=%.2f\n", int_oligo, suffix,
intl->hairpin_th);
/*Print out primer mispriming scores */
if (io_version == 3) {
if (seq_lib_num_seq(pa->p_args.repeat_lib) > 0) {
if (go_fwd == 1)
printf("PRIMER_LEFT%s_MISPRIMING_SCORE=%.2f, %s\n", suffix,
fwd->repeat_sim.score[fwd->repeat_sim.max],
fwd->repeat_sim.name);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_MISPRIMING_SCORE=%.2f, %s\n", suffix,
rev->repeat_sim.score[rev->repeat_sim.max],
rev->repeat_sim.name);
if (retval->output_type == primer_pairs)
printf("PRIMER_PAIR%s_MISPRIMING_SCORE=%.2f, %s\n", suffix,
retval->best_pairs.pairs[i].repeat_sim,
retval->best_pairs.pairs[i].rep_name);
}
/* Print out internal oligo mispriming scores */
if (go_int == 1 && seq_lib_num_seq(pa->o_args.repeat_lib) > 0)
printf("PRIMER_%s%s_MISHYB_SCORE=%.2f, %s\n", int_oligo, suffix,
intl->repeat_sim.score[intl->repeat_sim.max],
intl->repeat_sim.name);
} else {
if (seq_lib_num_seq(pa->p_args.repeat_lib) > 0) {
if (go_fwd == 1)
printf("PRIMER_LEFT%s_LIBRARY_MISPRIMING=%.2f, %s\n", suffix,
fwd->repeat_sim.score[fwd->repeat_sim.max],
fwd->repeat_sim.name);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_LIBRARY_MISPRIMING=%.2f, %s\n", suffix,
rev->repeat_sim.score[rev->repeat_sim.max],
rev->repeat_sim.name);
if (retval->output_type == primer_pairs)
printf("PRIMER_PAIR%s_LIBRARY_MISPRIMING=%.2f, %s\n", suffix,
retval->best_pairs.pairs[i].repeat_sim,
retval->best_pairs.pairs[i].rep_name);
}
/* Print out internal oligo mispriming scores */
if (go_int == 1 && seq_lib_num_seq(pa->o_args.repeat_lib) > 0)
printf("PRIMER_%s%s_LIBRARY_MISHYB=%.2f, %s\n", int_oligo, suffix,
intl->repeat_sim.score[intl->repeat_sim.max],
intl->repeat_sim.name);
}
/* If a sequence quality was provided, print it*/
if (NULL != sa->quality){
if (go_fwd == 1)
printf("PRIMER_LEFT%s_MIN_SEQ_QUALITY=%d\n", suffix,
fwd->seq_quality);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_MIN_SEQ_QUALITY=%d\n", suffix,
rev->seq_quality);
if (go_int == 1 && (retval->output_type == primer_list))
printf("PRIMER_%s%s_MIN_SEQ_QUALITY=%d\n", int_oligo, suffix,
intl->seq_quality);
/* Has to be here and in primer pairs for backward compatibility */
}
/* Print position penalty, this is for backward compatibility */
if (!_PR_DEFAULT_POSITION_PENALTIES(pa)
|| !PR_START_CODON_POS_IS_NULL(sa)){
printf("PRIMER_LEFT%s_POSITION_PENALTY=%f\n", suffix,
fwd->position_penalty);
printf("PRIMER_RIGHT%s_POSITION_PENALTY=%f\n", suffix,
rev->position_penalty);
}
/* Print primer end stability */
if (go_fwd == 1)
printf("PRIMER_LEFT%s_END_STABILITY=%.4f\n",
suffix, fwd->end_stability);
if (go_rev == 1)
printf("PRIMER_RIGHT%s_END_STABILITY=%.4f\n",
suffix, rev->end_stability);
/* Print primer template mispriming */
if ( (pa->thermodynamic_alignment == 0) && (go_fwd == 1) &&
(oligo_max_template_mispriming(fwd) != ALIGN_SCORE_UNDEF))
printf("PRIMER_LEFT%s_TEMPLATE_MISPRIMING=%.4f\n", suffix,
oligo_max_template_mispriming(fwd));
if ( (pa->thermodynamic_alignment == 0) && (go_rev == 1) &&
(oligo_max_template_mispriming(rev) != ALIGN_SCORE_UNDEF))
printf("PRIMER_RIGHT%s_TEMPLATE_MISPRIMING=%.4f\n", suffix,
oligo_max_template_mispriming(rev));
/* Print primer template mispriming thermodynamical approach*/
if ( (pa->thermodynamic_alignment == 1) && (go_fwd == 1) &&
(oligo_max_template_mispriming_thermod(fwd) != ALIGN_SCORE_UNDEF))
printf("PRIMER_LEFT%s_TEMPLATE_MISPRIMING_TH=%.4f\n", suffix,
oligo_max_template_mispriming_thermod(fwd));
if ( (pa->thermodynamic_alignment == 1) && (go_rev == 1) &&
(oligo_max_template_mispriming_thermod(rev) != ALIGN_SCORE_UNDEF))
printf("PRIMER_RIGHT%s_TEMPLATE_MISPRIMING_TH=%.4f\n", suffix,
oligo_max_template_mispriming_thermod(rev));
/************************************************************************************/
/* Print the pair parameters*/
if (retval->output_type == primer_pairs) {
if (go_int == 1 && NULL != sa->quality) /* FIX ME - Uptate the tests */
printf("PRIMER_%s%s_MIN_SEQ_QUALITY=%d\n", int_oligo,
suffix, intl->seq_quality);
/* Print pair comp_any */
if(pa->thermodynamic_alignment==0)
printf("PRIMER_PAIR%s_COMPL_ANY=%.2f\n", suffix,
retval->best_pairs.pairs[i].compl_any);
if(pa->thermodynamic_alignment==1)
printf("PRIMER_PAIR%s_COMPL_ANY_TH=%.2f\n", suffix,
retval->best_pairs.pairs[i].compl_any);
/* Print pair comp_end */
if(pa->thermodynamic_alignment==0)
printf("PRIMER_PAIR%s_COMPL_END=%.2f\n", suffix,
retval->best_pairs.pairs[i].compl_end);
if(pa->thermodynamic_alignment==1)
printf("PRIMER_PAIR%s_COMPL_END_TH=%.2f\n", suffix,
retval->best_pairs.pairs[i].compl_end);
if (io_version == 3) {
/* Print product size */
printf("PRIMER_PRODUCT_SIZE%s=%d\n", suffix,
retval->best_pairs.pairs[i].product_size);
/* Print the product Tm if a Tm range is defined */
if (pa->product_max_tm != PR_DEFAULT_PRODUCT_MAX_TM ||
pa->product_min_tm != PR_DEFAULT_PRODUCT_MIN_TM) {
printf("PRIMER_PRODUCT_TM%s=%.4f\n", suffix,
retval->best_pairs.pairs[i].product_tm);
printf("PRIMER_PRODUCT_TM_OLIGO_TM_DIFF%s=%.4f\n", suffix,
retval->best_pairs.pairs[i].product_tm_oligo_tm_diff);
printf("PRIMER_PAIR%s_T_OPT_A=%.4f\n", suffix,
retval->best_pairs.pairs[i].t_opt_a);
}
} else {
/* Print product size */
printf("PRIMER_PAIR%s_PRODUCT_SIZE=%d\n", suffix,
retval->best_pairs.pairs[i].product_size);
/* Print the product Tm if a Tm range is defined */
if (pa->product_max_tm != PR_DEFAULT_PRODUCT_MAX_TM ||
pa->product_min_tm != PR_DEFAULT_PRODUCT_MIN_TM) {
printf("PRIMER_PAIR%s_PRODUCT_TM=%.4f\n", suffix,
retval->best_pairs.pairs[i].product_tm);
printf("PRIMER_PAIR%s_PRODUCT_TM_OLIGO_TM_DIFF=%.4f\n", suffix,
retval->best_pairs.pairs[i].product_tm_oligo_tm_diff);
printf("PRIMER_PAIR%s_T_OPT_A=%.4f\n", suffix,
retval->best_pairs.pairs[i].t_opt_a);
}
}
/* Print the primer pair temlate mispriming */
if ((pa->thermodynamic_alignment == 0) && (retval->best_pairs.pairs[i].template_mispriming != ALIGN_SCORE_UNDEF))
printf("PRIMER_PAIR%s_TEMPLATE_MISPRIMING=%.2f\n", suffix,
retval->best_pairs.pairs[i].template_mispriming);
/* Print the primer pair temlate mispriming. Thermodynamic approach. */
if ((pa->thermodynamic_alignment == 1) && (retval->best_pairs.pairs[i].template_mispriming != ALIGN_SCORE_UNDEF))
printf("PRIMER_PAIR%s_TEMPLATE_MISPRIMING_TH=%.2f\n", suffix,
retval->best_pairs.pairs[i].template_mispriming);
} /* End of print parameters of primer pairs */
} /* End of the big loop printing all data */
/* End the print with newline and flush all buffers */
printf("=\n");
if (fflush(stdout) == EOF) {
perror("fflush(stdout) failed");
exit(-1);
}
}
static void
format_pairs(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const pair_array_t *best_pairs,
const char *pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
primer_rec *h = NULL;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
/* If there are errors, print them and return */
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name,
pr_append_str_chars(combined_retval_err));
return;
}
/* Print the sequence name if it is provided */
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
/* Print if a mispriming libraby was used and which one */
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
/* Print if a mispriming libraby for the internal oligo
* was used and which one */
if ( pa->pick_internal_oligo == 1 ) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal oligo mishyb library %s\n",
pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal oligo mishyb library specified\n");
}
/* Does the sequence start at position 0 or 1 ? */
fprintf(f, "Using %d-based sequence positions\n",
pa->first_base_index);
/* Complain if no primers are in the array */
if (best_pairs->num_pairs == 0) fprintf(f, "NO PRIMERS FOUND\n\n");
/* Print out the warings */
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "WARNING: %s\n\n", warning);
free(warning);
}
/* Print the results for the best pair */
print_summary(f, pa, sa, best_pairs, 0);
fprintf(f, "\n");
/* Print nicely out the sequence with the best pair */
if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
/* Print out the alternative pairs */
if (best_pairs->num_pairs > 1 ) print_rest(f, pa, sa, best_pairs);
/* Print the primer picking statistics */
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
/* Flush the buffers and return */
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
int
main(int argc, char *argv[]) {
/* Setup the input data structures handlers */
int format_output = 0;
int strict_tags = 0;
int dump_args = 0 ; /* set to 1 if dumping arguments to choose_primers */
int io_version = 4;
/* Some space for file names */
char *tmp_file_name = NULL;
char p3_all_file[FILE_NAME_SIZE];
char p3_settings_file[FILE_NAME_SIZE];
p3_global_settings *global_pa;
seq_args *sarg;
read_boulder_record_results read_boulder_record_res = {0,0};
pr_append_str fatal_parse_err;
pr_append_str nonfatal_parse_err;
/* Retval will point to the return value from choose_primers(). */
p3retval *retval = NULL;
int input_found=0;
p3_all_file[0] = '\0';
p3_settings_file[0] = '\0';
init_pr_append_str(&fatal_parse_err);
init_pr_append_str(&nonfatal_parse_err);
/* Get the program name for correct error messages */
pr_program_name = argv[0];
p3_set_program_name(pr_program_name);
/* We set up some signal handlers in case someone starts up the program
* from the command line, wonders why nothing is happening, and then kills
* the program. */
signal(SIGINT, sig_handler);
signal(SIGTERM, sig_handler);
/* Allocate the space for global settings and fill in default parameters */
global_pa = p3_create_global_settings();
if (!global_pa) {
exit(-2); /* Out of memory. */
}
if (dump_args) global_pa->dump = 1 ;
/* Read in the flags provided with the program call */
while (--argc > 0) {
argv++;
if (!strcmp(*argv, "-format_output")) {
format_output = 1;
} else if (!strcmp(*argv, "-about")) {
printf( "%s\n", pr_release);
exit (0);
} else if (!strcmp(*argv, "-2x_compat")) {
printf( "PRIMER_ERROR=flag -2x_compat is no longer supported\n=\n");
exit (-1);
} else if (!strcmp(*argv, "-io_version=3")) {
io_version = 3;
} else if (!strcmp(*argv, "-io_version=4")) {
io_version = 4;
} else if (!strncmp(*argv, "-p3_settings_file=", 18)) {
tmp_file_name = strchr(*argv,'=') + 1;
strncpy (p3_settings_file,tmp_file_name,FILE_NAME_SIZE-1);
} else if (!strcmp(*argv, "-strict_tags")) {
strict_tags = 1;
} else {
print_usage();
exit(-1);
}
}
/* Settings files have to be read in just below, and
the functions need a temporary sarg */
if (!(sarg = create_seq_arg())) {
exit(-2);
}
/* Read data from the settings file until a "=" line occurs. Assign parameter
* values for primer picking to pa and sa. */
if (p3_settings_file[0] != '\0') {
read_p3_file(p3_settings_file, settings, global_pa,
sarg, &fatal_parse_err, &nonfatal_parse_err,
&read_boulder_record_res);
}
/* We also need to print out errors here because the loop erases all
* errors at start */
/* If there are fatal errors, write the proper message and exit */
if (fatal_parse_err.data != NULL) {
if (format_output) {
format_error(stdout, sarg->sequence_name, fatal_parse_err.data);
} else {
print_boulder_error(fatal_parse_err.data);
}
fprintf(stderr, "%s: %s\n",
pr_program_name, fatal_parse_err.data);
destroy_seq_args(sarg);
exit(-4);
}
/* If there are nonfatal errors, write the proper message
* and skip to the end of the loop */
if (!pr_is_empty(&nonfatal_parse_err)) {
if (format_output) {
format_error(stdout, sarg->sequence_name,
nonfatal_parse_err.data);
} else {
print_boulder_error(nonfatal_parse_err.data);
}
}
/* The temporary sarg is not needed any more */
destroy_seq_args(sarg);
sarg = NULL;
/* Read the data from input stream record by record and process it if
* there are no errors. This is where the work is done. */
while (1) {
/* Create and initialize a seq_args data structure. sa (seq_args *) is
* initialized here because Values are _not_ retained across different
* input records. */
if (!(sarg = create_seq_arg())) {
exit(-2);
}
/* Reset all errors handlers and the return structure */
pr_set_empty(&fatal_parse_err);
pr_set_empty(&nonfatal_parse_err);
retval = NULL;
/* See read_boulder.h for documentation on read_boulder_record().*/
if (!read_boulder_record(stdin,
&strict_tags,
&io_version,
!format_output,
all_parameters,
global_pa,
sarg,
&fatal_parse_err,
&nonfatal_parse_err,
&read_boulder_record_res)) {
break; /* There were no more boulder records */
}
input_found = 1;
if ((global_pa->primer_task == pick_detection_primers)
&& (global_pa->pick_internal_oligo == 1)){
PR_ASSERT(global_pa->pick_internal_oligo);
}
/* If there are fatal errors, write the proper message and exit */
if (fatal_parse_err.data != NULL) {
if (format_output) {
format_error(stdout, sarg->sequence_name, fatal_parse_err.data);
} else {
print_boulder_error(fatal_parse_err.data);
}
fprintf(stderr, "%s: %s\n",
pr_program_name, fatal_parse_err.data);
destroy_p3retval(retval);
destroy_seq_args(sarg);
exit(-4);
}
/* If there are nonfatal errors, write the proper message
* and skip to the end of the loop */
if (!pr_is_empty(&nonfatal_parse_err)) {
if (format_output) {
format_error(stdout, sarg->sequence_name,
nonfatal_parse_err.data);
} else {
print_boulder_error(nonfatal_parse_err.data);
}
goto loop_wrap_up;
}
if (read_boulder_record_res.file_flag && sarg->sequence_name == NULL) {
/* We will not have a base name for the files */
if (format_output) {
format_error(stdout, NULL,
"Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0");
} else {
print_boulder_error("Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0");
}
goto loop_wrap_up;
}
/* Pick the primers - the central function */
p3_set_gs_primer_file_flag(global_pa,
read_boulder_record_res.file_flag);
retval = choose_primers(global_pa, sarg);
if (NULL == retval) exit(-2); /* Out of memory. */
/* This is old code to make it compatible with version 3 input.
In future versions it can be deleted!
If it was necessary to use a left_input, right_input,
or internal_oligo_input primer that was
unacceptable, then add warnings. */
if (global_pa->pick_anyway && (io_version == 3
|| format_output)) {
if (sarg->left_input) {
add_must_use_warnings(&retval->warnings,
"Left primer", &retval->fwd.expl);
}
if (sarg->right_input) {
add_must_use_warnings(&retval->warnings,
"Right primer", &retval->rev.expl);
}
if (sarg->internal_input) {
add_must_use_warnings(&retval->warnings,
"Hybridization probe", &retval->intl.expl);
}
}
/* End of the old code for compartibility. */
if (pr_is_empty(&retval->glob_err)
&& pr_is_empty(&retval->per_sequence_err)) {
/* We need to test for errors before we call
p3_print_oligo_lists. This function only works on retval as
returned when there were no errors. */
if (read_boulder_record_res.file_flag) {
/* Create files with left, right, and internal oligos. */
p3_print_oligo_lists(retval, sarg, global_pa,
&retval->per_sequence_err,
sarg->sequence_name);
}
}
if (format_output) {
print_format_output(stdout, &io_version, global_pa,
sarg, retval, pr_release,
read_boulder_record_res.explain_flag);
} else {
/* Use boulder output */
print_boulder(/* & */io_version, global_pa, sarg, retval,
read_boulder_record_res.explain_flag);
}
loop_wrap_up: /* Here the failed loops join in again */
if (NULL != retval) {
/* Check for errors and print them */
if (NULL != retval->glob_err.data) {
fprintf(stderr, "%s: %s\n", pr_program_name, retval->glob_err.data);
destroy_p3retval(retval);
destroy_seq_args(sarg);
exit(-4);
}
}
destroy_p3retval(retval); /* This works even if retval is NULL */
retval = NULL;
destroy_seq_args(sarg);
sarg = NULL;
} /* while (1) (processing boulder io records) ...
End of the primary working loop */
/* To avoid being distracted when looking for leaks: */
p3_destroy_global_settings(global_pa);
global_pa = NULL;
destroy_seq_args(sarg);
destroy_pr_append_str_data(&nonfatal_parse_err);
destroy_pr_append_str_data(&fatal_parse_err);
destroy_dpal_thal_arg_holder();
/* If it could not read input complain and die */
if (0 == input_found) {
print_usage();
exit(-3);
}
return 0;
}
int
main(int argc, char *argv[])
{
/* Setup the input data structures handlers */
int format_output = 0;
int strict_tags = 0;
int echo_settings = 0;
int dump_args = 0 ; /* set to 1 if dumping arguments to choose_primers */
int io_version = 4;
/* Some space for file names */
char p3_all_file[FILE_NAME_SIZE];
char p3_settings_file[FILE_NAME_SIZE];
p3_global_settings *global_pa;
seq_args *sarg;
read_boulder_record_results read_boulder_record_res = {0,0};
pr_append_str fatal_parse_err;
pr_append_str nonfatal_parse_err;
pr_append_str warnings;
/* Some variables needed by getopt */
int opt, option_index = 0;
struct option long_options[] = {
{"about", no_argument, 0, 'a'},
{"format_output", no_argument, &format_output, 1},
{"strict_tags", no_argument, &strict_tags, 1},
{"p3_settings_file", required_argument, 0, 'p'},
{"echo_settings_file", no_argument, &echo_settings, 1},
{"io_version", required_argument, 0, 'i'},
{"2x_compat", no_argument, 0, '2'},
{"output", required_argument, 0, 'o'},
{"error", required_argument, 0, 'e'},
{0, 0, 0, 0}
};
int about = 0, output = 0, error = 0, compat = 0, invalid_flag = 0;
char output_file[FILE_NAME_SIZE], error_file[FILE_NAME_SIZE];
/* Retval will point to the return value from choose_primers(). */
p3retval *retval = NULL;
int input_found=0;
p3_all_file[0] = '\0';
p3_settings_file[0] = '\0';
init_pr_append_str(&fatal_parse_err);
init_pr_append_str(&nonfatal_parse_err);
init_pr_append_str(&warnings);
/* Get the program name for correct error messages */
pr_release = libprimer3_release();
pr_program_name = argv[0];
p3_set_program_name(pr_program_name);
/* We set up some signal handlers in case someone starts up the program
* from the command line, wonders why nothing is happening, and then kills
* the program. */
signal(SIGINT, sig_handler);
signal(SIGTERM, sig_handler);
/* Allocate the space for global settings and fill in default parameters */
global_pa = p3_create_global_settings();
if (!global_pa) {
exit(-2); /* Out of memory. */
}
if (dump_args) global_pa->dump = 1 ;
/* Read in the flags provided with the program call */
opterr = 0;
while ((opt = getopt_long_only(argc, argv, "", long_options, &option_index)) != -1) {
switch (opt) {
case 'a':
about = 1;
break;
case 'p':
strncpy(p3_settings_file, optarg, FILE_NAME_SIZE - 1);
break;
case 'i':
if (!strcmp(optarg, "3"))
io_version = 3;
else if (!strcmp(optarg, "4"))
io_version = 4;
else
io_version = -1;
break;
case '2':
compat = 1;
break;
case 'o':
output = 1;
strncpy(output_file, optarg, FILE_NAME_SIZE - 1);
break;
case 'e':
error = 1;
strncpy(error_file, optarg, FILE_NAME_SIZE - 1);
break;
case '?':
invalid_flag = 1;
break;
}
}
/* Open the output and error files specified */
if (error == 1) {
/* reassign stderr */
if (freopen(error_file, "w", stderr) == NULL) {
fprintf(stderr, "Error creating file %s\n", error_file);
exit(-1);
}
}
if (output == 1) {
/* reassign stdout */
if (freopen(output_file, "w", stdout) == NULL) {
fprintf(stderr, "Error creating file %s\n", output_file);
exit(-1);
}
}
/* We do any printing after redirecting stdout and stderr */
if (about == 1) {
printf("%s\n", pr_release);
exit(0);
}
if ((io_version == -1) || (invalid_flag == 1)) {
print_usage();
exit(-1);
}
if (compat == 1) {
printf("PRIMER_ERROR=flag -2x_compat is no longer supported\n=\n");
exit(-1);
}
/* Check if an input file has been specified */
if (optind < argc) {
if (optind + 1 != argc) {
print_usage();
exit(-1);
}
if (freopen(argv[optind], "r", stdin) == NULL) {
fprintf(stderr, "Error opening file %s\n", argv[optind]);
exit(-1);
}
}
/* Settings files have to be read in just below, and
the functions need a temporary sarg */
if (!(sarg = create_seq_arg())) {
exit(-2);
}
/* Read data from the settings file until a "=" line occurs. Assign parameter
* values for primer picking to pa and sa. */
if (p3_settings_file[0] != '\0') {
read_p3_file(p3_settings_file, settings, echo_settings && !format_output,
global_pa, sarg, &fatal_parse_err,
&nonfatal_parse_err, &warnings, &read_boulder_record_res);
/* Check if the thermodynamical alignment flag was given */
if (global_pa->thermodynamic_alignment == 1)
read_thermodynamic_parameters();
}
/* We also need to print out errors here because the loop erases all
* errors at start */
/* If there are fatal errors, write the proper message and exit */
if (fatal_parse_err.data != NULL) {
if (format_output) {
format_error(stdout, sarg->sequence_name, fatal_parse_err.data);
} else {
print_boulder_error(fatal_parse_err.data);
}
fprintf(stderr, "%s: %s\n",
pr_program_name, fatal_parse_err.data);
destroy_seq_args(sarg);
exit(-4);
}
/* If there are nonfatal errors, write the proper message
* and skip to the end of the loop */
if (!pr_is_empty(&nonfatal_parse_err)) {
if (format_output) {
format_error(stdout, sarg->sequence_name,
nonfatal_parse_err.data);
} else {
print_boulder_error(nonfatal_parse_err.data);
}
}
/* The temporary sarg is not needed any more */
destroy_seq_args(sarg);
sarg = NULL;
/* Read the data from input stream record by record and process it if
* there are no errors. This is where the work is done. */
while (1) {
/* Create and initialize a seq_args data structure. sa (seq_args *) is
* initialized here because Values are _not_ retained across different
* input records. */
if (!(sarg = create_seq_arg())) {
exit(-2);
}
/* Reset all errors handlers and the return structure */
pr_set_empty(&fatal_parse_err);
pr_set_empty(&nonfatal_parse_err);
pr_set_empty(&warnings);
retval = NULL;
/* See read_boulder.h for documentation on read_boulder_record().*/
if (!read_boulder_record(stdin,
&strict_tags,
&io_version,
!format_output,
all_parameters,
global_pa,
sarg,
&fatal_parse_err,
&nonfatal_parse_err,
&warnings,
&read_boulder_record_res)) {
break; /* There were no more boulder records */
}
/* Check if the thermodynamical alignment flag was given and the path to the parameter files changed - we need to reread them */
if ((global_pa->thermodynamic_alignment == 1) && (thermodynamic_path_changed == 1))
read_thermodynamic_parameters();
input_found = 1;
if ((global_pa->primer_task == pick_detection_primers)
&& (global_pa->pick_internal_oligo == 1)){
PR_ASSERT(global_pa->pick_internal_oligo);
}
/* If there are fatal errors, write the proper message and exit */
if (fatal_parse_err.data != NULL) {
if (format_output) {
format_error(stdout, sarg->sequence_name, fatal_parse_err.data);
} else {
print_boulder_error(fatal_parse_err.data);
}
fprintf(stderr, "%s: %s\n",
pr_program_name, fatal_parse_err.data);
destroy_p3retval(retval);
destroy_seq_args(sarg);
exit(-4);
}
/* If there are nonfatal errors, write the proper message
* and skip to the end of the loop */
if (!pr_is_empty(&nonfatal_parse_err)) {
if (format_output) {
format_error(stdout, sarg->sequence_name,
nonfatal_parse_err.data);
} else {
print_boulder_error(nonfatal_parse_err.data);
}
goto loop_wrap_up;
}
/* Print any warnings and continue processing */
if (!pr_is_empty(&warnings)) {
if (format_output) {
format_warning(stdout, sarg->sequence_name,
warnings.data);
} else {
print_boulder_warning(warnings.data);
}
}
if (read_boulder_record_res.file_flag && sarg->sequence_name == NULL) {
/* We will not have a base name for the files */
if (format_output) {
format_error(stdout, NULL,
"Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0");
} else {
print_boulder_error("Need PRIMER_SEQUENCE_ID if PRIMER_FILE_FLAG is not 0");
}
goto loop_wrap_up;
}
/* Pick the primers - the central function */
p3_set_gs_primer_file_flag(global_pa,
read_boulder_record_res.file_flag);
retval = choose_primers(global_pa, sarg);
if (NULL == retval) exit(-2); /* Out of memory. */
/* This is old code to make it compatible with version 3 input.
In future versions it can be deleted!
If it was necessary to use a left_input, right_input,
or internal_oligo_input primer that was
unacceptable, then add warnings. */
if (global_pa->pick_anyway && (io_version == 3
|| format_output)) {
if (sarg->left_input) {
add_must_use_warnings(&retval->warnings,
"Left primer", &retval->fwd.expl);
}
if (sarg->right_input) {
add_must_use_warnings(&retval->warnings,
"Right primer", &retval->rev.expl);
}
if (sarg->internal_input) {
add_must_use_warnings(&retval->warnings,
"Hybridization probe", &retval->intl.expl);
}
}
/* End of the old code for compartibility. */
if (pr_is_empty(&retval->glob_err)
&& pr_is_empty(&retval->per_sequence_err)) {
/* We need to test for errors before we call
p3_print_oligo_lists. This function only works on retval as
returned when there were no errors. */
if (read_boulder_record_res.file_flag) {
/* Create files with left, right, and internal oligos. */
p3_print_oligo_lists(retval, sarg, global_pa,
&retval->per_sequence_err,
sarg->sequence_name);
}
}
if (format_output) {
print_format_output(stdout, &io_version, global_pa,
sarg, retval, pr_release,
read_boulder_record_res.explain_flag);
} else {
/* Use boulder output */
print_boulder(/* & */io_version, global_pa, sarg, retval,
read_boulder_record_res.explain_flag);
}
loop_wrap_up: /* Here the failed loops join in again */
if (NULL != retval) {
/* Check for errors and print them */
if (NULL != retval->glob_err.data) {
fprintf(stderr, "%s: %s\n", pr_program_name, retval->glob_err.data);
destroy_p3retval(retval);
destroy_seq_args(sarg);
exit(-4);
}
}
destroy_p3retval(retval); /* This works even if retval is NULL */
retval = NULL;
destroy_seq_args(sarg);
sarg = NULL;
} /* while (1) (processing boulder io records) ...
End of the primary working loop */
/* To avoid being distracted when looking for leaks: */
if (global_pa->thermodynamic_alignment == 1)
destroy_thal_structures();
p3_destroy_global_settings(global_pa);
global_pa = NULL;
destroy_seq_args(sarg);
destroy_pr_append_str_data(&nonfatal_parse_err);
destroy_pr_append_str_data(&fatal_parse_err);
destroy_pr_append_str_data(&warnings);
destroy_dpal_thal_arg_holder();
if (thermodynamic_params_path)
free(thermodynamic_params_path);
/* If it could not read input complain and die */
if (0 == input_found) {
print_usage();
exit(-3);
}
return 0;
}
static void
format_oligos(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const char* pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
int i;
int print_primers = 0;
primer_rec *h = NULL;
pair_array_t *best_pairs;
primer_rec *p;
int rest_count = 0;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
best_pairs = NULL;
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name, pr_append_str_chars(combined_retval_err));
return;
}
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
if (pa->pick_left_primer || pa->pick_right_primer) {
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
}
if (pa->pick_internal_oligo) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal probe mishyb library %s\n", pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal probe mishyb library specified\n");
}
fprintf(f, "Using %d-based sequence positions\n", pa->first_base_index);
if (pa->pick_left_primer) {
if (retval->fwd.num_elem == 0) {
fprintf(f, "NO LEFT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_internal_oligo) {
if (retval->intl.num_elem == 0) {
fprintf(f, "NO INTERNAL PROBE FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_right_primer) {
if (retval->rev.num_elem == 0) {
fprintf(f, "NO RIGHT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "\nWARNING: %s\n", warning);
free(warning);
}
if ((pa->primer_task != pick_primer_list ) && (pa->primer_task != pick_sequencing_primers)) {
if (print_primers == 1) {
print_oligo_header(f, "OLIGO", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
}
/* Print out the first line with the best primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > 0)) {
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->fwd.oligo;
rest_count = 1;
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > 0)) {
if(pa->modify_internal_oligo==1) {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
h = retval->intl.oligo;
rest_count = 1;
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > 0)) {
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->rev.oligo;
rest_count = 1;
}
}
if(print_primers == 1) {
fprintf(f, "SEQUENCE SIZE: %ld\n", (long int) strlen(sa->sequence));
fprintf(f, "INCLUDED REGION SIZE: %d\n\n", sa->incl_l);
if(sa->tar2.genotyping==0) {
print_pair_array(f, "TARGETS", sa->tar2.count, sa->tar2.pairs, pa, sa);
} else if(sa->tar2.genotyping==1) {
fprintf(f,"TARGET VARIANT * (position,size):");
if(sa->tar2.char_count==sa->tar2.VAR_sequence_number) {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]-1);
} else {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]);
}
fprintf(f,"\n\n");
}
print_pair_array(f, "EXCLUDED REGIONS", sa->excl2.count, sa->excl2.pairs, pa, sa);
print_pair_array(f, "INTERNAL PROBE EXCLUDED REGIONS", sa->excl_internal2.count, sa->excl_internal2.pairs, pa, sa);
print_2_pair_array(f, "PAIR_OK_REGIONS", sa->ok_regions.count, sa->ok_regions.left_pairs, sa->ok_regions.right_pairs, pa, sa);
}
if (pa->primer_task != pick_primer_list ) {
if(pa->pick_internal_oligo==1) {
if(print_seq(f,pa,sa,retval,retval->intl.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_left_primer==1) {
if(print_seq(f,pa,sa,retval,retval->fwd.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_right_primer==1) {
if(print_seq(f,pa,sa,retval,retval->rev.oligo,best_pairs,0)) exit(-2);
}
else if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
}
fprintf(f, "\n");
/* Print out the other primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > rest_count)) {
int n = retval->fwd.num_elem;
h = retval->fwd.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > rest_count)) {
int n = retval->intl.num_elem;
h = retval->intl.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_internal_oligo==1) {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > rest_count)) {
int n = retval->rev.num_elem;
h = retval->rev.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
