/* Assumes position is 0-based */
static char *
convert_to_chrpos_iit (unsigned int *chrpos, IIT_T chromosome_iit, unsigned int position) {
char *chromosome;
/* Subtract 1 to make 0-based */
chromosome = IIT_string_from_position(&(*chrpos),position-1U,chromosome_iit);
*chrpos += 1U; /* Bring back to 1-based */
IIT_free(&chromosome_iit);
return chromosome;
}
/* Assumes position is 0-based */
static char *
convert_to_chrpos (unsigned int *chrpos, char *genomesubdir, char *fileroot, unsigned int position) {
char *chromosome, *filename;
IIT_T chromosome_iit;
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
strlen(".chromosome.iit")+1,sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
if ((chromosome_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
/*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true)) == NULL) {
fprintf(stderr,"Can't read IIT file %s\n",filename);
exit(9);
}
FREE(filename);
/* Subtract 1 to make 0-based */
chromosome = IIT_string_from_position(&(*chrpos),position-1U,chromosome_iit);
*chrpos += 1U; /* Bring back to 1-based */
IIT_free(&chromosome_iit);
return chromosome;
}
int
main (int argc, char *argv[]) {
char *filename;
char *divstring = NULL, *lasttypestring, *ptr;
Univcoord_T univ_coordstart, univ_coordend;
Chrpos_T coordstart, coordend, lastcoord = 0U;
char Buffer[BUFLEN], nocomment[BUFLEN], query[BUFLEN], typestring[BUFLEN];
int typeint, *types, c;
int nargs, ntypes, ndivs;
int *value_matches = NULL, *matches = NULL;
int n_value_matches = 0, nmatches = 0, i;
int *leftflanks, *rightflanks, nleftflanks = 0, nrightflanks = 0;
long int total;
int n;
IIT_T iit = NULL;
Univ_IIT_T chromosome_iit = NULL;
bool skipp, universalp;
int opt;
extern int optind;
extern char *optarg;
const char *long_name;
int long_option_index = 0;
while ((opt = getopt_long(argc,argv,"a:b:f:LCASUu:c:HRTZN",long_options,&long_option_index)) != -1) {
switch (opt) {
case 0:
long_name = long_options[long_option_index].name;
if (!strcmp(long_name,"version")) {
print_program_version();
exit(0);
} else if (!strcmp(long_name,"help")) {
print_program_usage();
exit(0);
} else if (!strcmp(long_name,"exact")) {
exactp = true;
} else {
/* Shouldn't reach here */
fprintf(stderr,"Don't recognize option %s. For usage, run 'gsnap --help'",long_name);
exit(9);
}
break;
case 'a': lowval = atof(optarg); user_lowvalue_p = true; value_matches_p = true; break;
case 'b': highval = atof(optarg); user_highvalue_p = true; value_matches_p = true; break;
case 'f': fieldstring = optarg; break;
case 'L': force_label_p = true; break;
case 'C': force_coords_p = true; break;
case 'A': annotationonlyp = true; break;
case 'S': sortp = true; break;
case 'U': signedp = false; break;
case 'u': nflanking = atoi(optarg); break;
case 'c': centerp = true; centerlength = atoi(optarg); break;
case 'H': centeruc = true; break;
case 'R': runlengthp = true; break;
case 'T': tallyp = true; break;
case 'Z': zeroesp = true; break;
case 'N': statsp = true; break;
case 'V': print_program_version(); exit(0);
case '?': print_program_usage(); exit(0);
default: exit(9);
}
}
argc -= (optind - 1);
argv += (optind - 1);
if (argc <= 1) {
fprintf(stderr,"Need to specify an iit file. Type \"iit_get --help\" for help.\n");
exit(9);
} else {
filename = argv[1];
}
if (value_matches_p == true) {
if ((iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,
/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
if (IIT_valuep(iit) == false) {
fprintf(stderr,"Error: This IIT file does not have values stored\n");
exit(9);
}
if (user_lowvalue_p == true && user_highvalue_p == true) {
if (lowval > highval) {
fprintf(stderr,"Cannot have lowval %f > highval %f\n",lowval,highval);
exit(9);
} else {
value_matches = IIT_get_values_between(&n_value_matches,iit,lowval,highval,/*sortp*/false);
}
} else if (user_lowvalue_p == true) {
value_matches = IIT_get_values_above(&n_value_matches,iit,lowval,/*sortp*/false);
} else { /* user_highvalue_p == true */
value_matches = IIT_get_values_below(&n_value_matches,iit,highval,/*sortp*/false);
}
}
if (0 && statsp == true && argc == 2) {
/* Want total over entire IIT */
if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
/*labels_read_p*/false)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
total = 0;
n = 0;
for (i = 0; i < IIT_total_nintervals(iit); i++) {
debug(printf("index = %d\n",matches[i]));
compute_totals_tally(&total,&n,/*coordstart*/0,/*coordend*/-1U,i,iit);
}
printf("counts:%ld non-zero-positions:%u mean-over-nonzero:%.3f\n",total,n,(double) total/(double) n);
IIT_free(&iit);
return 0;
} else if ((universalp = IIT_universalp(filename,/*add_iit_p*/true)) == true) {
chromosome_iit = Univ_IIT_read(filename,/*readonlyp*/true,/*add_iit_p*/true);
if (argc != 3) {
fprintf(stderr,"For chromosome IIT file, need to specify a query on the command line\n");
exit(9);
} else {
/* Try as 0:<iitfile> 1:<query> */
matches = get_matches_univ(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&chromosome_iit,filename);
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval_univ(univ_coordstart,univ_coordend,matches[i],chromosome_iit);
}
}
if (divstring != NULL) {
FREE(divstring);
}
Univ_IIT_free(&chromosome_iit);
return 0;
} else if (argc == 2 && value_matches_p == true) {
/* Note: Could potentially handle input from stdin, but currently just deal with value_matches */
ndivs = IIT_ndivs(iit);
for (i = 0; i < n_value_matches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval(&lastcoord,/*total*/0,/*divstring*/NULL,/*coordstart*/0,/*coordend*/0,
value_matches[i],iit,ndivs,fieldint);
}
FREE(value_matches);
IIT_free(&iit);
return 0;
} else if (argc == 2) {
debug(printf("Running under argc 2\n"));
/* Expecting input from stdin */
if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
/*labels_read_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
while (fgets(Buffer,BUFLEN,stdin) != NULL) {
if ((ptr = rindex(Buffer,'\n')) != NULL) {
*ptr = '\0';
}
strcpy(nocomment,Buffer);
if ((ptr = rindex(nocomment,'#')) != NULL) {
*ptr = '\0';
}
skipp = false;
if ((nargs = sscanf(nocomment,"%s %s",query,typestring)) == 2) {
debug(printf("typestring is %s\n",typestring));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
query,typestring,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (nargs == 1) {
debug(printf("typestring is NULL\n"));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
query,/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
fprintf(stderr,"Can't parse line %s. Ignoring.\n",nocomment);
skipp = true;
}
total = 0;
if (skipp == false) {
fprintf(stdout,"# Query: %s\n",Buffer);
ndivs = IIT_ndivs(iit);
if (nflanking > 0) {
for (i = nleftflanks-1; i >= 0; i--) {
debug(printf("\nleft index = %d\n",leftflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,leftflanks[i],iit,ndivs,fieldint);
}
printf("====================\n");
FREE(leftflanks);
}
lastcoord = coordstart;
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
total = print_interval(&lastcoord,total,divstring,coordstart,coordend,matches[i],iit,ndivs,fieldint);
}
if (nflanking > 0) {
printf("====================\n");
for (i = 0; i < nrightflanks; i++) {
debug(printf("\nright index = %d\n",rightflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,rightflanks[i],iit,ndivs,fieldint);
}
FREE(rightflanks);
}
if (zeroesp == true) {
while (lastcoord <= coordend) {
printf("%s\t%u\t%d\n",divstring,lastcoord,0);
lastcoord++;
}
}
}
if (divstring != NULL) {
FREE(divstring);
}
FREE(matches);
printf("%ld\n",total);
fprintf(stdout,"# End\n");
fflush(stdout);
}
IIT_free(&iit);
return 0;
} else {
/* Get coordinates/type from command line */
if (argc == 3) {
/* Try as 0:<iitfile> 1:<query> */
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (argc == 4) {
/* Try as 0:<iitfile> 1:<query> 2:<type> */
debug(printf("Running under argc 4\n"));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],argv[3],&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
types = (int *) CALLOC(argc-3,sizeof(int));
for (c = 3, ntypes = 0; c < argc; c++) {
if ((typeint = IIT_typeint(iit,argv[c])) < 0) {
fprintf(stderr,"No such type as %s. Ignoring the type.\n",argv[c]);
} else {
types[ntypes++] = typeint;
lasttypestring = argv[c];
}
}
if (ntypes == 0) {
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (ntypes == 1) {
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],lasttypestring,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
matches = get_matches_multiple_typed(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],types,ntypes,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
}
}
if (value_matches_p == true) {
matches = match_intersection(&nmatches,/*matches1*/matches,/*nmatches1*/nmatches,
/*matches2*/value_matches,/*nmatches2*/n_value_matches);
FREE(value_matches);
}
#if 0
if (centerp == true) {
print_spaces(centerlength);
printf("*");
print_spaces(centerlength-1);
printf("\n");
}
#endif
if (statsp == true) {
total = 0;
n = 0;
for (i = 0; i < nmatches; i++) {
debug(printf("index = %d\n",matches[i]));
compute_totals_tally(&total,&n,coordstart,coordend,matches[i],iit);
}
n = coordend - coordstart + 1;
printf("counts:%ld width:%u mean:%.3f\n",total,n,(double)total/(double) n);
#if 0
} else if (geomeanp == true) {
logtotal = 0.0;
total = 0;
n = 0;
for (i = 0; i < nmatches; i++) {
debug(printf("index = %d\n",matches[i]));
logtotal = compute_logtotal_tally(&total,&n,coordstart,coordend,matches[i],iit);
}
printf("geomean:%f totalcounts:%ld posrange:%d\n",
exp(logtotal/(double) (coordend - coordstart + 1)) - 1.0,total,n);
#endif
} else {
ndivs = IIT_ndivs(iit);
if (nflanking > 0) {
for (i = nleftflanks-1; i >= 0; i--) {
debug(printf("\nleft index = %d\n",leftflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,leftflanks[i],iit,ndivs,fieldint);
}
printf("====================\n");
FREE(leftflanks);
}
lastcoord = coordstart;
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,matches[i],iit,ndivs,fieldint);
}
if (nflanking > 0) {
printf("====================\n");
for (i = 0; i < nrightflanks; i++) {
debug(printf("\nright index = %d\n",rightflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,rightflanks[i],iit,ndivs,fieldint);
}
FREE(rightflanks);
}
}
if (divstring != NULL) {
FREE(divstring);
}
FREE(matches);
IIT_free(&iit);
return 0;
}
}
bool
Parserange_universal_iit (char **div, bool *revcomp,
Genomicpos_T *genomicstart, Genomicpos_T *genomiclength,
Genomicpos_T *chrstart, Genomicpos_T *chrend,
Genomicpos_T *chroffset, Genomicpos_T *chrlength,
char *query, IIT_T chromosome_iit, IIT_T contig_iit) {
char *coords;
Genomicpos_T result, left, length;
Interval_T interval;
int theindex;
int rc;
*revcomp = false;
if (index(query,':')) {
/* Segment must be a genome, chromosome, or contig */
debug(printf("Parsed query %s into ",query));
*div = strtok(query,":");
if ((*div)[0] == '+') {
*revcomp = false;
*div = &((*div)[1]);
} else if ((*div)[0] == '_') {
*revcomp = true;
*div = &((*div)[1]);
}
coords = strtok(NULL,":");
debug(printf("segment %s and coords %s\n",*div,coords));
debug(printf("Interpreting segment %s as a chromosome\n",*div));
if (coords == NULL) {
debug(printf(" entire chromosome\n"));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left=0,length=0,chromosome_iit);
} else if (isnumberp(&result,coords)) {
debug(printf(" and coords %s as a number\n",coords));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left=result-1,length=1,chromosome_iit);
} else if (isrange(&left,&length,&(*revcomp),coords)) {
debug(printf(" and coords %s as a range starting at %u with length %u and revcomp = %d\n",
coords,left,length,*revcomp));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left,length,chromosome_iit);
} else {
debug(printf(" but coords %s is neither a number nor a range\n",coords));
rc = -1;
}
/* Compute chromosomal coordinates */
*chrstart = left;
*chrend = *chrstart + *genomiclength;
*chrstart += 1U; /* Make 1-based */
/* Get chromosomal information */
if ((theindex = IIT_find_one(chromosome_iit,*div)) < 0) {
fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",*div);
/* exit(9); */
} else {
interval = IIT_interval(chromosome_iit,theindex);
*chroffset = Interval_low(interval);
*chrlength = Interval_length(interval);
}
if (rc != 0) {
/* Try contig */
debug(printf("Interpreting segment %s as a contig\n",*div));
if (isnumberp(&result,coords)) {
debug(printf(" and coords %s as a number\n",coords));
rc = translate_contig(&(*genomicstart),&(*genomiclength),*div,left=result-1,length=1,contig_iit);
} else if (isrange(&left,&length,&(*revcomp),coords)) {
debug(printf(" and coords %s as a range starting at %u with length %u and revcomp = %d\n",
coords,left,length,*revcomp));
rc = translate_contig(&(*genomicstart),&(*genomiclength),*div,left,length,contig_iit);
} else {
debug(printf(" but coords %s is neither a number nor a range\n",coords));
rc = -1;
}
}
if (rc != 0) {
fprintf(stderr,"Can't find coordinates %s:%s\n",*div,coords);
return false;
} else {
return true;
}
} else {
/* Query must be a genomic position, genomic range, or contig */
*chrstart = *chroffset = *chrlength = 0;
debug(printf("Parsed query %s as atomic ",query));
if (isnumberp(&result,query)) {
debug(printf("number\n"));
*genomicstart = result-1;
*genomiclength = 1;
} else if (isrange(&left,&length,&(*revcomp),query)) {
debug(printf("range\n"));
*genomicstart = left;
*genomiclength = length;
} else {
debug(printf("contig\n"));
return false;
#if 0
rc = translate_contig(&(*genomicstart),&(*genomiclength),query,left=0,length=0,contig_iit);
IIT_free(&contig_iit);
#endif
}
*div = convert_to_chrpos_iit(&(*chrstart),chromosome_iit,*genomicstart);
*chrend = *chrstart + *genomiclength;
*chrstart += 1U; /* Make 1-based */
/* Try chromosome first */
if ((theindex = IIT_find_one(chromosome_iit,*div)) < 0) {
fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",*div);
return false;
} else {
interval = IIT_interval(chromosome_iit,theindex);
*chroffset = Interval_low(interval);
*chrlength = Interval_length(interval);
return true;
}
}
}
bool
Parserange_universal (char **div, bool *revcomp,
Genomicpos_T *genomicstart, Genomicpos_T *genomiclength,
Genomicpos_T *chrstart, Genomicpos_T *chrend,
Genomicpos_T *chroffset, Genomicpos_T *chrlength,
char *query, char *genomesubdir, char *fileroot) {
char *coords, *filename;
Genomicpos_T result, left, length;
IIT_T chromosome_iit, contig_iit;
Interval_T interval;
int theindex;
int rc;
*revcomp = false;
if (index(query,':')) {
/* Segment must be a genome, chromosome, or contig */
debug(printf("Parsed query %s into ",query));
*div = strtok(query,":");
if ((*div)[0] == '+') {
*revcomp = false;
*div = &((*div)[1]);
} else if ((*div)[0] == '_') {
*revcomp = true;
*div = &((*div)[1]);
}
coords = strtok(NULL,":");
debug(printf("segment %s and coords %s\n",*div,coords));
/* Try chromosome first */
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
strlen(".chromosome.iit")+1,sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
chromosome_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
/*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
FREE(filename);
debug(printf("Interpreting segment %s as a chromosome\n",*div));
if (coords == NULL) {
debug(printf(" entire chromosome\n"));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left=0,length=0,chromosome_iit);
} else if (isnumberp(&result,coords)) {
debug(printf(" and coords %s as a number\n",coords));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left=result-1,length=1,chromosome_iit);
} else if (isrange(&left,&length,&(*revcomp),coords)) {
debug(printf(" and coords %s as a range starting at %u with length %u and revcomp = %d\n",
coords,left,length,*revcomp));
rc = translate_chromosomepos_universal(&(*genomicstart),&(*genomiclength),*div,left,length,chromosome_iit);
} else {
debug(printf(" but coords %s is neither a number nor a range\n",coords));
rc = -1;
}
/* Compute chromosomal coordinates */
*chrstart = left;
*chrend = *chrstart + *genomiclength;
*chrstart += 1U; /* Make 1-based */
/* Get chromosomal information */
if ((theindex = IIT_find_one(chromosome_iit,*div)) < 0) {
fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",*div);
/* exit(9); */
} else {
interval = IIT_interval(chromosome_iit,theindex);
*chroffset = Interval_low(interval);
*chrlength = Interval_length(interval);
}
IIT_free(&chromosome_iit);
#if 0
/* Contig IIT's are of type 1, which require some work to compute
on current div-based scheme. Just abandoning for now. */
if (rc != 0) {
/* Try contig */
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
strlen(".contig.iit")+1,sizeof(char));
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
contig_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
/*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
FREE(filename);
debug(printf("Interpreting segment %s as a contig\n",*div));
if (coords == NULL) {
debug(printf(" entire contig\n"));
rc = translate_contig_universal(&(*genomicstart),&(*genomiclength),*div,left=0,length=0,chromosome_iit);
} else if (isnumberp(&result,coords)) {
debug(printf(" and coords %s as a number\n",coords));
rc = translate_contig(&(*genomicstart),&(*genomiclength),*div,left=result-1,length=1,contig_iit);
} else if (isrange(&left,&length,&(*revcomp),coords)) {
debug(printf(" and coords %s as a range starting at %u with length %u and revcomp = %d\n",
coords,left,length,*revcomp));
rc = translate_contig(&(*genomicstart),&(*genomiclength),*div,left,length,contig_iit);
} else {
debug(printf(" but coords %s is neither a number nor a range\n",coords));
rc = -1;
}
IIT_free(&contig_iit);
}
#endif
if (rc != 0) {
fprintf(stderr,"Can't find coordinates %s:%s\n",*div,coords);
return false;
} else {
return true;
}
} else {
/* Query must be a genomic position, genomic range, or contig */
*chrstart = *chroffset = *chrlength = 0;
debug(printf("Parsed query %s as atomic ",query));
if (isnumberp(&result,query)) {
debug(printf("number\n"));
*genomicstart = result-1;
*genomiclength = 1;
} else if (isrange(&left,&length,&(*revcomp),query)) {
debug(printf("range\n"));
*genomicstart = left;
*genomiclength = length;
} else {
debug(printf("contig\n"));
return false;
#if 0
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
strlen(".contig.iit")+1,sizeof(char));
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
contig_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
/*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
FREE(filename);
rc = translate_contig(&(*genomicstart),&(*genomiclength),query,left=0,length=0,contig_iit);
IIT_free(&contig_iit);
#endif
}
*div = convert_to_chrpos(&(*chrstart),genomesubdir,fileroot,*genomicstart);
*chrend = *chrstart + *genomiclength;
*chrstart += 1U; /* Make 1-based */
/* Try chromosome first */
filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(fileroot)+
strlen(".chromosome.iit")+1,sizeof(char));
sprintf(filename,"%s/%s.chromosome.iit",genomesubdir,fileroot);
chromosome_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
/*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
FREE(filename);
if ((theindex = IIT_find_one(chromosome_iit,*div)) < 0) {
fprintf(stderr,"Cannot find chromosome %s in chromosome IIT file\n",*div);
IIT_free(&chromosome_iit);
return false;
} else {
interval = IIT_interval(chromosome_iit,theindex);
*chroffset = Interval_low(interval);
*chrlength = Interval_length(interval);
IIT_free(&chromosome_iit);
return true;
}
}
}
bool
Parserange_query (char **divstring, unsigned int *coordstart, unsigned int *coordend, bool *revcomp,
char *query, char *filename) {
char *coords;
unsigned int result, left, length;
int div_strlen;
IIT_T iit;
*divstring = NULL;
*revcomp = false;
if ((coords = find_div(&div_strlen,query,':')) != NULL) {
/* Query may have a div */
*divstring = (char *) CALLOC(div_strlen+1,sizeof(char));
strncpy(*divstring,query,div_strlen);
debug(printf("Parsed query %s into divstring %s and coords %s\n",
query,*divstring,coords));
if (IIT_read_divint(filename,*divstring,/*add_iit_p*/true) < 0) {
fprintf(stderr,"Chromosome %s not found in IIT file\n",*divstring);
debug(printf(" but divstring not found, so treat as label\n"));
FREE(*divstring); /* free only when returning false */
return false;
} else if (coords == NULL || *coords == '\0') {
debug(printf(" entire div\n"));
if ((iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ONE,*divstring,
/*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else {
*coordstart= 0;
*coordend = IIT_divlength(iit,*divstring);
debug(printf(" divlength is %u\n",*coordend));
IIT_free(&iit);
}
return true;
} else if (isnumberp(&result,coords)) {
debug(printf(" and coords %s as a number\n",coords));
*coordstart = result;
*coordend = result;
return true;
} else if (isrange(&left,&length,&(*revcomp),coords)) {
debug(printf(" and coords %s as a range starting at %u with length %u and revcomp = %d\n",
coords,left,length,*revcomp));
*coordstart = left + 1; /* Because isrange is 0-based */
*coordend = left + length;
return true;
} else {
debug(printf(" but coords %s is neither a number nor a range. Interpret as a label.\n",coords));
FREE(*divstring); /* free only when returning false */
return false;
}
} else {
/* No div. Query must be a number, range, or label */
debug(printf("Parsed query %s without a div ",query));
if (isnumberp(&result,query)) {
debug(printf("number\n"));
*coordstart = result;
*coordend = result;
return true;
} else if (isrange(&left,&length,&(*revcomp),query)) {
debug(printf("range\n"));
*coordstart = left + 1; /* Because isrange is 0-based */
*coordend = left + length;
return true;
} else {
debug(printf("label\n"));
return false;
}
}
}
