static void
write_contig_file (char *genomesubdir, char *fileroot, Table_T accsegmentpos_table,
Tableint_T chrlength_table, List_T contigtypelist) {
FILE *textfp;
char *textfile, *iitfile, *annot;
int naccessions, i;
char **accessions, *divstring;
Segmentpos_T segmentpos;
Chrom_T chrom;
Genomicpos_T chroffset, universalpos1, universalpos2;
List_T divlist = NULL, intervallist = NULL, labellist = NULL, annotlist = NULL, p;
Table_T intervaltable, labeltable, annottable;
Interval_T interval;
#if 0
void **keys;
int *values, ntypes;
#endif
if (divsort == NO_SORT) {
accessions = (char **) Table_keys_by_timeindex(accsegmentpos_table,NULL);
naccessions = Table_length(accsegmentpos_table);
} else {
/* Get accessions in order */
accessions = (char **) Table_keys(accsegmentpos_table,NULL);
naccessions = Table_length(accsegmentpos_table);
current_accsegmentpos_table = accsegmentpos_table;
qsort(accessions,naccessions,sizeof(char *),bysegmentpos_compare);
}
#if 0
/* Get types in order */
keys = Tableint_keys(contigtype_table,NULL);
values = Tableint_values(contigtype_table,0);
ntypes = Tableint_length(contigtype_table);
contigtypes = (char **) CALLOC(ntypes+1,sizeof(char *)); /* Add 1 for type 0 */
contigtypes[0] = "";
for (j = 0; j < ntypes; j++) {
contigtypes[values[j]] = keys[j];
}
FREE(values);
FREE(keys);
#endif
/* Write contig text file */
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".contig")+1,sizeof(char));
sprintf(textfile,"%s/%s.contig",genomesubdir,fileroot);
/* Use binary, not text, so files are Unix-compatible */
if ((textfp = FOPEN_WRITE_BINARY(textfile)) == NULL) {
fprintf(stderr,"Can't write to file %s\n",textfile);
exit(9);
}
FREE(textfile);
for (i = 0; i < naccessions; i++) {
segmentpos = (Segmentpos_T) Table_get(accsegmentpos_table,(void *) accessions[i]);
chrom = Segmentpos_chrom(segmentpos);
chroffset = (Genomicpos_T) Tableint_get(chrlength_table,chrom);
universalpos1 = chroffset + Segmentpos_chrpos1(segmentpos);
universalpos2 = chroffset + Segmentpos_chrpos2(segmentpos);
/* Print as 1-based, inclusive [a,b] */
if (Segmentpos_revcompp(segmentpos) == true) {
fprintf(textfp,"%s\t%u..%u\t%s:%u..%u\t%u",
accessions[i],universalpos2+1U,universalpos1,
Chrom_string(chrom),Segmentpos_chrpos2(segmentpos)+1U,Segmentpos_chrpos1(segmentpos),
Segmentpos_length(segmentpos));
} else {
fprintf(textfp,"%s\t%u..%u\t%s:%u..%u\t%u",
accessions[i],universalpos1+1U,universalpos2,
Chrom_string(chrom),Segmentpos_chrpos1(segmentpos)+1U,Segmentpos_chrpos2(segmentpos),
Segmentpos_length(segmentpos));
}
#if 0
if (Segmentpos_type(segmentpos) > 0) {
fprintf(textfp,"\t%s",contigtypes[Segmentpos_type(segmentpos)]);
}
#endif
fprintf(textfp,"\n");
/* Store as 0-based, inclusive [a,b] */
labellist = List_push(labellist,(void *) accessions[i]);
if (Segmentpos_revcompp(segmentpos) == true) {
/* The negative sign in the interval is the indication that the
contig was reverse complement */
intervallist = List_push(intervallist,
(void *) Interval_new(universalpos2-1U,universalpos1,
Segmentpos_type(segmentpos)));
} else {
intervallist = List_push(intervallist,
(void *) Interval_new(universalpos1,universalpos2-1U,
Segmentpos_type(segmentpos)));
}
#if 0
/* IIT version 1 */
sprintf(seglength,"%u",Segmentpos_length(segmentpos));
annot = (char *) CALLOC(strlen(seglength)+1,sizeof(char));
strcpy(annot,seglength);
#else
/* IIT versions >= 2 */
annot = (char *) CALLOC(1,sizeof(char));
annot[0] = '\0';
#endif
annotlist = List_push(annotlist,(void *) annot);
}
fclose(textfp);
#if 0
FREE(contigtypes);
#endif
FREE(accessions);
intervallist = List_reverse(intervallist);
/* contigtypelist = List_reverse(contigtypelist); -- Done by caller */
labellist = List_reverse(labellist);
annotlist = List_reverse(annotlist);
/* Write contig IIT file */
divstring = (char *) CALLOC(1,sizeof(char));
divstring[0] = '\0';
divlist = List_push(NULL,divstring);
intervaltable = Table_new(65522,Table_string_compare,Table_string_hash);
labeltable = Table_new(65522,Table_string_compare,Table_string_hash);
annottable = Table_new(65522,Table_string_compare,Table_string_hash);
Table_put(intervaltable,(void *) divstring,intervallist);
Table_put(labeltable,(void *) divstring,labellist);
Table_put(annottable,(void *) divstring,annotlist);
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".contig.iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.contig.iit",genomesubdir,fileroot);
#if 0
debug(
for (p = contigtypelist; p != NULL; p = List_next(p)) {
printf("Type %s\n",(char *) List_head(p));
}
);
int main(void) {
List_T L = NULL;
Bootstrap(); // Need to initialize library
printf("============> Start List Tests\n\n");
printf("=> Test0: create\n");
{
L = List_new();
assert(L);
List_free(&L);
}
printf("=> Test0: OK\n\n");
printf("=> Test1: List_push() & List_length()\n");
{
L = List_new();
List_push(L, "1");
List_push(L, "2");
List_push(L, "3");
List_push(L, "4");
List_push(L, "5");
List_push(L, "6");
List_push(L, "7");
List_push(L, "8");
List_push(L, "9");
List_push(L, "10");
List_push(L, "11");
List_push(L, "12");
List_push(L, "13");
List_push(L, "14");
List_push(L, "15");
assert(Str_isEqual(L->tail->e, "1"));
assert(Str_isEqual(L->head->e, "15"));
assert(List_length(L) == 15);
}
printf("=> Test1: OK\n\n");
printf("=> Test2: List_pop()\n");
{
int i= 0;
list_t p;
while (List_pop(L)) ;
assert(List_length(L) == 0);
// Ensure that nodes are retained in the freelist
for (p= L->freelist; p; p= p->next) i++;
assert(i == 15);
List_free(&L);
}
printf("=> Test2: OK\n\n");
printf("=> Test3: List_append()\n");
{
L = List_new();
List_append(L, "1");
List_append(L, "2");
List_append(L, "3");
List_append(L, "4");
List_append(L, "5");
List_append(L, "6");
List_append(L, "7");
List_append(L, "8");
List_append(L, "9");
List_append(L, "10");
List_append(L, "11");
List_append(L, "12");
List_append(L, "13");
List_append(L, "14");
List_append(L, "15");
assert(Str_isEqual(L->tail->e, "15"));
assert(Str_isEqual(L->head->e, "1"));
assert(List_length(L) == 15);
}
printf("=> Test3: OK\n\n");
printf("=> Test4: List_cat()\n");
{
List_T t= List_new();
List_append(t, "a");
List_append(t, "b");
List_append(t, "c");
List_append(t, "d");
List_cat(L, t);
assert(Str_isEqual(L->tail->e, "d"));
assert(Str_isEqual(L->head->e, "1"));
assert(List_length(L) == 19);
}
printf("=> Test4: OK\n\n");
printf("=> Test5: List_reverse()\n");
{
list_t p;
List_T l= List_new();
List_append(l, "a");
List_append(l, "b");
List_append(l, "c");
List_append(l, "d");
printf("\tList before reverse: ");
for (p= l->head; p; p= p->next)
printf("%s%s", (char*)p->e, p->next?"->":"\n");
assert(Str_isEqual(l->head->e, "a"));
assert(Str_isEqual(l->tail->e, "d"));
List_reverse(l);
printf("\tList after reverse: ");
for (p= l->head; p; p= p->next)
printf("%s%s", (char*)p->e, p->next?"->":"\n");
assert(Str_isEqual(l->head->e, "d"));
assert(Str_isEqual(l->tail->e, "a"));
List_free(&l);
}
printf("=> Test5: OK\n\n");
printf("=> Test6: List_map()\n");
{
int i = 0;
List_map(L, apply, &i);
assert(i == 19);
}
printf("=> Test6: OK\n\n");
printf("=> Test7: List_clear()\n");
{
List_clear(L);
assert(List_length(L) == 0);
assert(L->freelist);
}
printf("=> Test7: OK\n\n");
List_free(&L);
printf("=> Test8: List malloc\n");
{
L = List_new();
List_push(L, "1");
List_push(L, "2");
List_push(L, "3");
List_push(L, "4");
List_push(L, "5");
List_push(L, "6");
List_push(L, "7");
List_push(L, "8");
List_push(L, "9");
List_push(L, "10");
List_push(L, "11");
List_push(L, "12");
List_push(L, "13");
List_push(L, "14");
List_push(L, "15");
assert(Str_isEqual(L->tail->e, "1"));
assert(Str_isEqual(L->head->e, "15"));
assert(List_length(L) == 15);
List_clear(L);
List_append(L, "1");
List_append(L, "2");
List_append(L, "3");
List_append(L, "4");
List_append(L, "5");
List_append(L, "6");
List_append(L, "7");
List_append(L, "8");
List_append(L, "9");
List_append(L, "10");
List_append(L, "11");
List_append(L, "12");
List_append(L, "13");
List_append(L, "14");
List_append(L, "15");
assert(Str_isEqual(L->tail->e, "15"));
assert(Str_isEqual(L->head->e, "1"));
assert(List_length(L) == 15);
List_free(&L);
}
printf("=> Test8: OK\n\n");
printf("=> Test9: List remove\n");
{
char *one = "1";
char *two = "2";
L = List_new();
printf("\tRemove from empty list.. ");
assert(List_remove(L, "1") == NULL);
printf("OK\n");
List_push(L, one);
printf("\tRemove from 1 element list.. ");
assert(List_remove(L, one) == one);
assert(List_length(L) == 0);
printf("OK\n");
List_push(L, one);
List_push(L, two);
printf("\tRemove last from list.. ");
assert(List_remove(L, two) == two);
assert(List_length(L) == 1);
printf("OK\n");
List_append(L, two);
List_append(L, two);
List_append(L, two);
List_append(L, "5");
printf("\tRemove first occurrence.. ");
assert(List_remove(L, two) == two);
assert(List_length(L) == 4);
printf("OK\n");
List_free(&L);
}
printf("=> Test9: OK\n\n");
printf("=> Test10: check pointers\n");
{
L = List_new();
printf("\tCheck pop.. ");
List_push(L, "1");
List_push(L, "2");
List_pop(L);
List_pop(L);
List_push(L, "1");
assert(L->head == L->tail);
List_pop(L);
List_append(L, "1");
assert(L->head == L->tail);
printf("OK\n");
printf("\tCheck remove.. ");
List_push(L, "1");
List_append(L, "2");
List_remove(L, "2");
List_remove(L, "1");
assert(L->head == L->tail);
printf("OK\n");
List_free(&L);
}
printf("=> Test10: OK\n\n");
printf("=> Test11: List_toArray()\n");
{
List_T l = List_new();
List_append(l, "a");
List_append(l, "b");
List_append(l, "c");
List_append(l, "d");
char **array = (char**)List_toArray(l);
assert(Str_isEqual(array[0], "a"));
assert(Str_isEqual(array[1], "b"));
assert(Str_isEqual(array[2], "c"));
assert(Str_isEqual(array[3], "d"));
assert(array[4] == NULL);
FREE(array);
List_free(&l);
}
printf("=> Test11: OK\n\n");
printf("============> List Tests: OK\n\n");
return 0;
}
/* Modifies chrlength_table to store offsets, rather than chrlengths */
static void
write_chromosome_file (char *genomesubdir, char *fileroot, Tableint_T chrlength_table) {
FILE *textfp, *chrsubsetfp;
char *divstring, *textfile, *chrsubsetfile, *iitfile, *chr_string, emptystring[1];
int n, i;
Chrom_T *chroms;
Genomicpos_T chroffset = 0, chrlength;
List_T divlist = NULL;
List_T intervallist = NULL, chrtypelist = NULL, labellist = NULL, annotlist = NULL, p;
Table_T intervaltable, labeltable, annottable;
Interval_T interval;
emptystring[0] = '\0';
if (divsort == NO_SORT) {
chroms = (Chrom_T *) Tableint_keys_by_timeindex(chrlength_table,0U);
n = Tableint_length(chrlength_table);
} else {
/* Get chromosomes in order */
chroms = (Chrom_T *) Tableint_keys(chrlength_table,0U);
n = Tableint_length(chrlength_table);
switch (divsort) {
case ALPHA_SORT: qsort(chroms,n,sizeof(Chrom_T),Chrom_compare_alpha); break;
case NUMERIC_ALPHA_SORT: qsort(chroms,n,sizeof(Chrom_T),Chrom_compare_numeric_alpha); break;
case CHROM_SORT: qsort(chroms,n,sizeof(Chrom_T),Chrom_compare_chrom); break;
default: abort();
}
}
/* Write chromosome text file and chrsubset file */
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".chromosome")+1,sizeof(char));
sprintf(textfile,"%s/%s.chromosome",genomesubdir,fileroot);
/* Use binary, not text, so files are Unix-compatible */
if ((textfp = FOPEN_WRITE_BINARY(textfile)) == NULL) {
fprintf(stderr,"Can't write to file %s\n",textfile);
exit(9);
}
FREE(textfile);
chrsubsetfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".chrsubset")+1,sizeof(char));
sprintf(chrsubsetfile,"%s/%s.chrsubset",genomesubdir,fileroot);
/* Use binary, not text, so files are Unix-compatible */
if ((chrsubsetfp = FOPEN_WRITE_BINARY(chrsubsetfile)) == NULL) {
fprintf(stderr,"Can't write to file %s\n",chrsubsetfile);
exit(9);
}
FREE(chrsubsetfile);
fprintf(chrsubsetfp,">all\n");
fprintf(chrsubsetfp,"\n");
chrtypelist = List_push(chrtypelist,"");
for (i = 0; i < n; i++) {
chrlength = (Genomicpos_T) Tableint_get(chrlength_table,chroms[i]);
assert(chroffset <= chroffset+chrlength-1);
chr_string = Chrom_string(chroms[i]);
if (i < 100) {
fprintf(stderr,"Chromosome %s has universal coordinates %u..%u\n",
chr_string,chroffset+1,chroffset+1+chrlength-1);
} else if (i == 100) {
fprintf(stderr,"More than 100 contigs. Will stop printing messages\n");
}
if (n <= 100) {
fprintf(chrsubsetfp,">%s\n",chr_string);
fprintf(chrsubsetfp,"+%s\n",chr_string);
}
fprintf(textfp,"%s\t%u..%u\t%u\n",
chr_string,chroffset+1,chroffset+chrlength,chrlength);
intervallist = List_push(intervallist,(void *) Interval_new(chroffset,chroffset+chrlength-1U,0));
labellist = List_push(labellist,(void *) chr_string);
annotlist = List_push(annotlist,(void *) emptystring); /* No annotations */
Tableint_put(chrlength_table,chroms[i],chroffset);
chroffset += chrlength;
}
FREE(chroms);
intervallist = List_reverse(intervallist);
labellist = List_reverse(labellist);
fclose(chrsubsetfp);
fclose(textfp);
/* Write chromosome IIT file */
divstring = (char *) CALLOC(1,sizeof(char));
divstring[0] = '\0';
divlist = List_push(NULL,divstring);
intervaltable = Table_new(65522,Table_string_compare,Table_string_hash);
labeltable = Table_new(65522,Table_string_compare,Table_string_hash);
annottable = Table_new(65522,Table_string_compare,Table_string_hash);
Table_put(intervaltable,(void *) divstring,intervallist);
Table_put(labeltable,(void *) divstring,labellist);
Table_put(annottable,(void *) divstring,annotlist);
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
IIT_write(iitfile,divlist,chrtypelist,/*fieldlist*/(List_T) NULL,
intervaltable,labeltable,annottable,divsort,
/*version, use 1 for backward compatibility*/1,
/*label_pointers_8p*/false,/*annot_pointers_8p*/false);
FREE(iitfile);
List_free(&divlist);
FREE(divstring);
Table_free(&annottable);
Table_free(&labeltable);
Table_free(&intervaltable);
List_free(&annotlist);
/* Do not free strings in labellist, since they are not allocated */
List_free(&labellist);
/* chrtypelist has no dynamically allocated strings */
List_free(&chrtypelist);
for (p = intervallist; p != NULL; p = List_next(p)) {
interval = (Interval_T) List_head(p);
Interval_free(&interval);
}
List_free(&intervallist);
return;
}
