/* 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;
}
/* Puts reference genome into refgenome_fp (assume compressed),
and puts alternate strain sequences into altstrain_iit. */
static void
genome_write_memory (FILE *refgenome_fp, FILE *input,
IIT_T contig_iit, IIT_T altstrain_iit, UINT4 *genomecomp,
unsigned int nuint4, char *fileroot) {
char Buffer[BUFFERSIZE], Complement[BUFFERSIZE], *segment;
char *accession, *p;
Genomicpos_T leftposition, rightposition, startposition, endposition, truelength,
maxposition = 0, currposition = 0;
int contigtype;
bool revcompp;
#ifdef ALTSTRAIN
int altstrain_index, altstrain_offset;
#endif
int nbadchars = 0;
int ncontigs = 0;
while (fgets(Buffer,BUFFERSIZE,input) != NULL) {
if (Buffer[0] == '>') {
/* HEADER */
accession = parse_accession(Buffer);
find_positions(&revcompp,&leftposition,&rightposition,&startposition,&endposition,
&truelength,&contigtype,accession,contig_iit);
if (++ncontigs < 50) {
if (revcompp == true) {
fprintf(stderr,"Writing contig %s to universal coordinates %u..%u in genome %s\n",
accession,startposition,endposition,fileroot);
} else {
fprintf(stderr,"Writing contig %s to universal coordinates %u..%u in genome %s\n",
accession,startposition+1U,endposition+1U,fileroot);
}
} else if (ncontigs == 50) {
fprintf(stderr,"More than 50 contigs. Will stop printing messages\n");
}
if (contigtype > 0) {
#ifdef ALTSTRAIN
fprintf(stderr," (alternate strain %s)",IIT_typestring(altstrain_iit,contigtype));
#endif
}
FREE(accession);
if (contigtype > 0) {
#ifdef ALTSTRAIN
/* Initialize file pointer for alternate strain */
altstrain_index = IIT_get_exact(altstrain_iit,/*divstring*/NULL,leftposition,rightposition,contigtype);
if (revcompp == true) {
altstrain_offset = rightposition + 1U - leftposition;
} else {
altstrain_offset = 0;
}
debug(printf("Setting altstrain_offset to be %d\n",altstrain_offset));
#endif
}
/* Handles case where true length is greater than provided
coordinates. This needs to be after call to IIT_get_exact */
if (leftposition + truelength - 1U > rightposition) {
debug(fprintf(stderr,"Extending endposition for truelength of %u\n",truelength));
rightposition = leftposition + truelength;
if (revcompp == true) {
endposition = startposition - truelength;
} else {
endposition = startposition + truelength;
}
}
/* In both cases, set file pointer for reference strain,
although we won't write sequence of alternate strain. For an
alternate strain, ensure that we fill the reference strain
with sufficient X's. */
if (startposition > maxposition) {
/* Start beyond end of file */
debug(printf("Filling with X's from %u to %u-1\n",maxposition,startposition));
fill_x_memory(genomecomp,maxposition,startposition);
if (contigtype > 0) {
#ifdef ALTSTRAIN
fill_x_memory(genomecomp,leftposition,rightposition + 1);
maxposition = currposition = rightposition + 1;
#endif
} else {
maxposition = rightposition;
currposition = startposition;
}
} else {
/* Start within file */
if (contigtype > 0) {
#ifdef ALTSTRAIN
if (rightposition + 1 > maxposition) {
debug(printf("Filling with X's from %u to %u-1\n",maxposition,rightposition+1));
fill_x_memory(genomecomp,maxposition,rightposition + 1);
maxposition = currposition = rightposition + 1;
}
#endif
} else {
debug(printf("Moving to %u\n",startposition));
currposition = startposition;
}
}
} else {
/* SEQUENCE */
if ((p = rindex(Buffer,'\n')) != NULL) {
*p = '\0';
}
if ((p = rindex(Buffer,CONTROLM)) != NULL) {
*p = '\0';
}
if (revcompp == true) {
make_complement_buffered(Complement,Buffer,strlen(Buffer));
segment = Complement;
} else {
segment = Buffer;
}
if (contigtype > 0) {
#ifdef ALTSTRAIN
/* Write alternate strain */
if (revcompp == true) {
altstrain_offset -= strlen(segment);
debug(printf("Writing alternate strain at %u\n",altstrain_offset));
IIT_backfill_sequence(altstrain_iit,altstrain_index,altstrain_offset,segment);
} else {
debug(printf("Writing alternate strain at %u\n",altstrain_offset));
IIT_backfill_sequence(altstrain_iit,altstrain_index,altstrain_offset,segment);
altstrain_offset += strlen(segment);
}
#endif
} else {
/* Write reference strain */
if (revcompp == true) {
debug(printf("Filling with sequence from %u-1 to %u\n",currposition,currposition-strlen(segment)));
currposition -= strlen(segment);
nbadchars = Compress_update_memory(nbadchars,genomecomp,segment,currposition,currposition+strlen(segment));
} else {
debug(printf("Filling with sequence from %u to %u-1\n",currposition,currposition+strlen(segment)));
nbadchars = Compress_update_memory(nbadchars,genomecomp,segment,currposition,currposition+strlen(segment));
currposition += strlen(segment);
if (currposition > maxposition) {
maxposition = currposition;
}
}
}
}
}
move_absolute(refgenome_fp,0U);
FWRITE_UINTS(genomecomp,nuint4,refgenome_fp);
fprintf(stderr,"A total of %d non-ACGTNX characters were seen in the genome.\n",nbadchars);
return;
}
/* 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;
}
/* Permits arbitrary ASCII characters. Useful for storing numeric data */
static void
genome_writeraw_file (FILE *refgenome_fp, FILE *input,
IIT_T contig_iit, IIT_T altstrain_iit, char *fileroot, int index1part) {
char Buffer[BUFFERSIZE], Reverse[BUFFERSIZE], *segment;
char *accession, c;
Genomicpos_T leftposition, rightposition, startposition, endposition, truelength,
maxposition = 0, currposition = 0;
int contigtype;
int strlength;
int i;
bool revcompp;
#ifdef ALTSTRAIN
int altstrain_index, altstrain_offset;
#endif
int ncontigs = 0;
for (i = 0; i < WRITEBLOCK; i++) {
Empty[i] = 0;
}
while (fgets(Buffer,BUFFERSIZE,input) != NULL) {
if (Buffer[0] != '>') {
fprintf(stderr,"Expecting to see a new FASTA entry\n");
fprintf(stderr,"Instead, saw %d (%c)\n",(int) Buffer[0],Buffer[0]);
exit(9);
} else {
/* HEADER */
accession = parse_accession(Buffer);
find_positions(&revcompp,&leftposition,&rightposition,&startposition,&endposition,
&truelength,&contigtype,accession,contig_iit);
if (++ncontigs < 50) {
if (revcompp == true) {
fprintf(stderr,"Writing contig %s to universal coordinates %u..%u in genome %s\n",
accession,startposition,endposition,fileroot);
} else {
fprintf(stderr,"Writing contig %s to universal coordinates %u..%u in genome %s\n",
accession,startposition+1U,endposition+1U,fileroot);
}
} else if (ncontigs == 50) {
fprintf(stderr,"More than 50 contigs. Will stop printing messages\n");
}
if (contigtype > 0) {
#ifdef ALTSTRAIN
fprintf(stderr," (alternate strain %s)",IIT_typestring(altstrain_iit,contigtype));
#endif
}
FREE(accession);
if (contigtype > 0) {
#ifdef ALTSTRAIN
/* Initialize file pointer for alternate strain */
altstrain_index = IIT_get_exact(altstrain_iit,/*divstring*/NULL,leftposition,rightposition,contigtype);
if (revcompp == true) {
altstrain_offset = rightposition + 1U - leftposition;
} else {
altstrain_offset = 0;
}
debug(printf("Setting altstrain_offset to be %d\n",altstrain_offset));
#endif
}
/* Handles case where true length is greater than provided
coordinates. This needs to be after call to IIT_get_exact */
if (leftposition + truelength - 1U > rightposition) {
debug(fprintf(stderr,"Extending endposition for truelength of %u\n",truelength));
rightposition = leftposition + truelength;
if (revcompp == true) {
endposition = startposition - truelength;
} else {
endposition = startposition + truelength;
}
}
/* In both cases, set file pointer for reference strain,
although we won't write sequence of alternate strain. For an
alternate strain, ensure that we fill the reference strain
with sufficient X's. */
if (startposition > maxposition) {
/* Start beyond end of file */
debug(printf("Filling with zeroes from %u to %u-1\n",maxposition,startposition));
fill_zero(refgenome_fp,maxposition,startposition,/*uncompressedp*/true,index1part);
if (contigtype > 0) {
#ifdef ALTSTRAIN
fill_zero(refgenome_fp,leftposition,rightposition + 1,/*uncompressedp*/true,index1part);
maxposition = currposition = rightposition + 1;
#endif
} else {
maxposition = rightposition;
currposition = startposition;
}
} else {
/* Start within file */
if (contigtype > 0) {
#ifdef ALTSTRAIN
if (rightposition + 1 > maxposition) {
debug(printf("Filling with zeroes from %u to %u-1\n",maxposition,rightposition+1));
fill_zero(refgenome_fp,maxposition,rightposition + 1,/*uncompressedp*/true,index1part);
maxposition = currposition = rightposition + 1;
}
#endif
} else {
debug(printf("Moving to %u\n",startposition));
move_absolute(refgenome_fp,startposition);
currposition = startposition;
}
}
/* SEQUENCE */
fprintf(stderr,"Processing %u characters\n",truelength);
while (truelength > 0) {
if (truelength > BUFFERSIZE) {
if ((strlength = fread(Buffer,sizeof(char),BUFFERSIZE,input)) < BUFFERSIZE) {
fprintf(stderr,"Expecting %u more characters, but saw end of file\n",truelength);
exit(9);
}
truelength -= BUFFERSIZE;
} else {
if ((strlength = fread(Buffer,sizeof(char),truelength,input)) < truelength) {
fprintf(stderr,"Expecting %u more characters, but saw end of file\n",truelength);
exit(9);
}
truelength = 0;
}
if (revcompp == true) {
make_reverse_buffered(Reverse,Buffer,strlength);
segment = Reverse;
} else {
segment = Buffer;
}
if (contigtype > 0) {
#ifdef ALTSTRAING
/* Write alternate strain. It is likely that IIT commands
will fail because they depend on \0 to terminate the segment. */
if (revcompp == true) {
altstrain_offset -= strlength;
debug(printf("Writing alternate strain at %u\n",altstrain_offset));
IIT_backfill_sequence(altstrain_iit,altstrain_index,altstrain_offset,segment);
} else {
debug(printf("Writing alternate strain at %u\n",altstrain_offset));
IIT_backfill_sequence(altstrain_iit,altstrain_index,altstrain_offset,segment);
altstrain_offset += strlength;
}
#endif
} else {
/* Write reference strain */
if (revcompp == true) {
debug(printf("Filling with sequence from %u-1 to %u\n",currposition,currposition-strlength));
currposition -= strlength;
fwrite(segment,sizeof(char),strlength,refgenome_fp);
} else {
debug(printf("Filling with sequence from %u to %u-1\n",currposition,currposition+strlength));
fwrite(segment,sizeof(char),strlength,refgenome_fp);
currposition += strlength;
if (currposition > maxposition) {
maxposition = currposition;
}
}
}
}
if ((c = fgetc(input)) != EOF && c != '\n') {
fprintf(stderr,"Expecting linefeed at end of sequence. Saw %d instead\n",
c);
exit(9);
}
}
}
return;
}
