C++ (Cpp) IIT_version Examples

Example #1

File: genome-write.c Project: fabiocpn/GMAP-GSNAP

static void
find_positions (bool *revcompp, Genomicpos_T *leftposition, Genomicpos_T *rightposition,
		Genomicpos_T *startposition, Genomicpos_T *endposition, Genomicpos_T *truelength,
		int *contigtype, char *accession, IIT_T contig_iit) {
  int index;
  Interval_T interval;
  char firstchar;

  if ((index = IIT_find_one(contig_iit,accession)) == -1) {
    fprintf(stderr,"Can't find accession %s in contig IIT file\n",
	    accession);
    exit(9);
  } else {	
    interval = IIT_interval(contig_iit,index);

    *leftposition = Interval_low(interval);
    *rightposition = Interval_high(interval);

    if (IIT_version(contig_iit) <= 1) {
      firstchar = IIT_annotation_firstchar(contig_iit,index);
      if (firstchar == '-') {
	*revcompp = true;
	*startposition = Interval_high(interval) + 1U;
	*endposition = Interval_low(interval) + 1U;
      } else {
	*revcompp = false;
	*startposition = Interval_low(interval);
	*endposition = Interval_high(interval);
      }
    } else {
      if (Interval_sign(interval) < 0) {
	*revcompp = true;
	*startposition = Interval_high(interval) + 1U;
	*endposition = Interval_low(interval) + 1U;
      } else {
	*revcompp = false;
	*startposition = Interval_low(interval);
	*endposition = Interval_high(interval);
      }
    }

    *truelength = Interval_length(interval);
    *contigtype = Interval_type(interval);
    debug(printf("revcompp = %d, leftposition = %d, rightposition = %d, startposition = %d, endposition = %d\n",
		 *revcompp,*leftposition,*rightposition,*startposition,*endposition));
    return;
  }
}

Example #2

File: iit_get.c Project: djinnome/JAMg-1

/* 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;
}