static int
translate_chromosomepos_universal (unsigned int *genomicstart, unsigned int *genomiclength,
char *chromosome, unsigned int left, unsigned int length,
IIT_T chromosome_iit) {
int rc = 1, index;
Interval_T interval;
#ifdef DEBUG
bool allocp;
#endif
if ((index = IIT_find_linear(chromosome_iit,chromosome)) >= 0) {
debug(printf("chromosome %s => index %d\n",chromosome,index));
interval = IIT_interval(chromosome_iit,index);
debug(printf(" => label %s with interval low %u\n",
IIT_label(chromosome_iit,index,&allocp),Interval_low(interval)));
*genomicstart = Interval_low(interval)+left;
if (*genomicstart < Interval_low(interval)) {
fprintf(stderr,"%u + %u = %u (exceeds a 32-bit unsigned int)\n",
Interval_low(interval),left,*genomicstart);
exit(9);
}
if (length == 0) {
*genomiclength = Interval_length(interval)-left;
} else {
*genomiclength = length;
}
rc = 0;
}
return rc;
}
static char
check_acgt (char nt, IIT_T snps_iit, int divno, int i) {
int index;
char *label;
bool allocp;
if (nt == 'N') {
return nt;
} else if (nt != 'A' && nt != 'C' && nt != 'G' && nt != 'T') {
index = IIT_index(snps_iit,divno,i);
label = IIT_label(snps_iit,index,&allocp);
fprintf(stderr,"\nFor %s, alternate allele %c is not ACGT, so using 'N' as alternate allele",
label,nt);
if (allocp) {
FREE(label);
}
return 'N';
} else {
return nt;
}
}
/* Need to store just the part of the query specified (e.g., 1..10) */
static void
print_interval_runlength (Chrpos_T *lastcoord, char *divstring, Chrpos_T coordstart, Chrpos_T coordend,
int indexi, IIT_T iit, bool zeroesp) {
Interval_T interval;
char *label;
bool allocp;
Chrpos_T chrpos, intervalend;
int value;
label = IIT_label(iit,indexi,&allocp);
value = atoi(label);
interval = IIT_interval(iit,indexi);
chrpos = Interval_low(interval);
intervalend = Interval_high(interval);
if (zeroesp == true) {
while (*lastcoord < chrpos) {
printf("%s\t%u\t%d\n",divstring,*lastcoord,0);
(*lastcoord)++;
}
}
while (chrpos < coordstart) {
chrpos++;
}
while (chrpos <= intervalend && chrpos <= coordend) {
printf("%s\t%u\t%d\n",divstring,chrpos,value);
chrpos++;
}
*lastcoord = chrpos;
if (allocp == true) {
FREE(label);
}
return;
}
/* coordstart used only if centerp or tallyp is true */
static long int
print_interval (Chrpos_T *lastcoord, long int total,
char *divstring, Chrpos_T coordstart, Chrpos_T coordend,
int index, IIT_T iit, int ndivs, int fieldint) {
Interval_T interval;
char *label, *annotation, *restofheader;
bool allocp;
if (centerp == true) {
print_interval_centered(divstring,coordstart,index,iit,fieldint);
return 0;
} else if (tallyp == true) {
total += print_interval_tally(&(*lastcoord),divstring,coordstart,coordend,index,iit,zeroesp);
return total;
} else if (runlengthp == true) {
print_interval_runlength(&(*lastcoord),divstring,coordstart,coordend,index,iit,zeroesp);
return 0;
}
if (annotationonlyp == false) {
label = IIT_label(iit,index,&allocp);
printf(">%s ",label);
if (allocp == true) {
FREE(label);
}
if (ndivs > 1) {
if (divstring == NULL) {
/* For example, if interval was retrieved by label */
divstring = IIT_divstring_from_index(iit,index);
}
printf("%s:",divstring);
}
debug(printf("index is %d\n",index));
interval = IIT_interval(iit,index);
if (signedp == false) {
printf("%u..%u",Interval_low(interval),Interval_high(interval));
} else if (Interval_sign(interval) < 0) {
printf("%u..%u",Interval_high(interval),Interval_low(interval));
} else {
printf("%u..%u",Interval_low(interval),Interval_high(interval));
}
if (Interval_type(interval) > 0) {
printf(" %s",IIT_typestring(iit,Interval_type(interval)));
}
#if 0
/* Unnecessary because of "\n" after restofheader below */
if (IIT_version(iit) < 5) {
printf("\n");
}
#endif
}
if (fieldint < 0) {
annotation = IIT_annotation(&restofheader,iit,index,&allocp);
printf("%s\n",restofheader);
printf("%s",annotation);
if (allocp == true) {
FREE(restofheader);
}
} else {
annotation = IIT_annotation(&restofheader,iit,index,&allocp);
printf("%s\n",restofheader);
if (allocp == true) {
FREE(restofheader);
}
annotation = IIT_fieldvalue(iit,index,fieldint);
printf("%s\n",annotation);
FREE(annotation);
}
return 0;
}
/* Need to store just the part of the query specified (e.g., 1..10) */
static void
print_interval_centered (char *divstring, Chrpos_T coordstart, int index, IIT_T iit, int fieldint) {
Interval_T interval;
char *label, *annotation, *restofheader, centerchar;
bool allocp;
int annotlength, left, centerpos;
if (fieldint < 0) {
annotation = IIT_annotation(&restofheader,iit,index,&allocp);
if (allocp == true) {
FREE(restofheader);
}
} else {
annotation = IIT_fieldvalue(iit,index,fieldint);
allocp = true;
}
annotlength = strlen(annotation);
if (annotation[annotlength-1] == '\n') {
annotlength--;
}
interval = IIT_interval(iit,index);
left = coordstart - Interval_low(interval); /* + length(query) - queryend */
if (Interval_sign(interval) < 0) {
centerpos = annotlength-left-1;
} else {
centerpos = left;
}
centerchar = annotation[centerpos];
if (centeruc == true && islower(centerchar)) {
if (fieldint >= 0 && allocp == true) {
FREE(annotation);
}
} else {
print_spaces(centerlength-left);
if (Interval_sign(interval) < 0) {
print_complement(annotation,annotlength-1,centerpos+1);
printf("[%c]",complCode[(int) centerchar]);
print_complement(annotation,centerpos-1,0);
} else {
print_forward(annotation,0,centerpos-1);
printf("[%c]",centerchar);
print_forward(annotation,centerpos+1,annotlength-1);
}
print_spaces(centerlength+left-annotlength);
if (fieldint >= 0 && allocp == true) {
FREE(annotation);
}
printf("\t");
if (Interval_type(interval) > 0) {
printf("%s\t",IIT_typestring(iit,Interval_type(interval)));
}
if (divstring != NULL) {
if (Interval_sign(interval) < 0) {
printf("-%s:",divstring);
} else {
printf("+%s:",divstring);
}
}
if (signedp == false) {
printf("%u..%u",Interval_low(interval),Interval_high(interval));
} else if (Interval_sign(interval) < 0) {
printf("%u..%u",Interval_high(interval),Interval_low(interval));
} else {
printf("%u..%u",Interval_low(interval),Interval_high(interval));
}
printf("\t");
label = IIT_label(iit,index,&allocp);
printf("%s",label);
if (allocp == true) {
FREE(label);
}
printf("\n");
}
return;
}
