int test1 (void) {
struct tagbstring t = bsStatic ("Hello world");
bstring b, c, d;
int ret = 0;
printf ("TEST: bTail and bHead functions.\n");
b = bTail (&t, 5);
c = bHead (&t, 5);
ret += 0 >= biseqcstr (b, "world");
ret += 0 >= biseqcstr (c, "Hello");
bdestroy (b);
bdestroy (c);
b = bTail (&t, 0);
c = bHead (&t, 0);
ret += 0 >= biseqcstr (b, "");
ret += 0 >= biseqcstr (c, "");
bdestroy (b);
bdestroy (c);
d = bstrcpy (&t);
b = bTail (d, 5);
c = bHead (d, 5);
ret += 0 >= biseqcstr (b, "world");
ret += 0 >= biseqcstr (c, "Hello");
bdestroy (b);
bdestroy (c);
bdestroy (d);
printf ("\t# failures: %d\n", ret);
return ret;
}
END_TEST
START_TEST(core_001)
{
struct tagbstring t = bsStatic("Hello world");
bstring b, c, d;
int ret = 0;
b = bTail(&t, 5);
ck_assert(b != NULL);
c = bHead(&t, 5);
ck_assert(c != NULL);
ret = biseqcstr(b, "world");
ck_assert_int_eq(ret, 1);
ret = biseqcstr(c, "Hello");
ck_assert_int_eq(ret, 1);
ret = bdestroy(b);
ck_assert_int_eq(ret, BSTR_OK);
ret = bdestroy(c);
ck_assert_int_eq(ret, BSTR_OK);
b = bTail(&t, 0);
ck_assert(b != NULL);
c = bHead(&t, 0);
ck_assert(c != NULL);
ret = biseqcstr(b, "");
ck_assert_int_eq(ret, 1);
ret = biseqcstr(c, "");
ck_assert_int_eq(ret, 1);
ret = bdestroy(b);
ck_assert_int_eq(ret, BSTR_OK);
ret = bdestroy(c);
ck_assert_int_eq(ret, BSTR_OK);
d = bstrcpy(&t);
ck_assert(d != NULL);
b = bTail(d, 5);
ck_assert(b != NULL);
c = bHead(d, 5);
ck_assert(c != NULL);
ret = biseqcstr(b, "world");
ck_assert_int_eq(ret, 1);
ret = biseqcstr(c, "Hello");
ck_assert_int_eq(ret, 1);
ret = bdestroy(b);
ck_assert_int_eq(ret, BSTR_OK);
ret = bdestroy(c);
ck_assert_int_eq(ret, BSTR_OK);
ret = bdestroy(d);
ck_assert_int_eq(ret, BSTR_OK);
}
Action *Action_create(const char *profile)
{
Action *action = calloc(sizeof(Action), 1);
check_mem(action);
action->profile_dir = bfromcstr(profile);
action->name = bTail(action->profile_dir,
blength(action->profile_dir) -
bstrrchr(action->profile_dir, '/') - 1);
action->depends = Profile_read_setting(action->profile_dir, "depends");
return action;
error:
return NULL;
}
/**
* Argument:
* fn - file names
* Return:
* An ordered file names.
*/
alder_seqid_file_t * alder_seqid_file_init(struct bstrList *fn)
{
// Test if all of the files exist.
// Determine the file type (text or gzip).
// Use the first line to determine file formats (FASTA or FASTQ).
// Read the first sequence name of each file.
// Pair files using sequence names.
alder_seqid_file_t *v = malloc(sizeof(alder_seqid_file_t));
int numberOfFile = fn->qty;
v->filename = bstrVectorCreate(numberOfFile);
v->type = malloc(numberOfFile * sizeof(int));
v->format = malloc(numberOfFile * sizeof(int));
v->pair = malloc(numberOfFile * sizeof(int));
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_exist(bdata(fn->entry[i]));
if (s == 0) {
alder_seqid_file_free(v);
return NULL;
}
}
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_isgzip(bdata(fn->entry[i]));
if (s == 1) {
v->type[i] = 2;
} else {
v->type[i] = 1;
}
}
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_whatformat(bdata(fn->entry[i]));
if (s == 1) {
v->format[i] = 1;
} else if (s == 2) {
v->format[i] = 2;
} else {
alder_seqid_file_free(v);
return NULL;
}
}
struct bstrList *bnames = bstrVectorCreate(fn->qty);
for (int i = 0; i < fn->qty; i++) {
bstring s = alder_file_firstline(bdata(fn->entry[i]));
int posFirstSpace = bstrchrp(s, ' ', 0);
bstring bword = NULL;
if (posFirstSpace != BSTR_ERR) {
bword = bHead(s, posFirstSpace);
} else {
bword = bstrcpy(s);
}
bdestroy(s);
bstring bname = bTail(bword, bword->slen - 1);
bdestroy(bword);
bstrVectorAdd(bnames, bdata(bname));
bdestroy(bname);
}
for (int i = 0; i < fn->qty; i++) {
v->pair[i] = -1;
for (int j = 0; j < fn->qty; j++) {
if (i == j) continue;
if (!bstrcmp(bnames->entry[i], bnames->entry[j])) {
v->pair[i] = j;
}
}
}
int *pairCount = malloc(numberOfFile * sizeof(int));
memset(pairCount, 0, numberOfFile*sizeof(int));
for (int i = 0; i < fn->qty; i++) {
int j = v->pair[i];
pairCount[j]++;
}
for (int i = 0; i < fn->qty; i++) {
if (pairCount[i] > 1) {
free(pairCount);
alder_seqid_file_free(v);
return NULL;
}
}
free(pairCount);
///////////////////////////////////////////////////////////////////////////
// Order pairs.
int pairI = 0;
alder_vector_pair_t * pair = alder_vector_pair_t_alloc(fn->qty);
for (int i = 0; i < fn->qty; i++) {
if (v->pair[i] >= 0) {
int alreadPaired = 0;
for (int j = 0; j < pairI; j++) {
if (pair->data[j].first == i ||
pair->data[j].second== i) {
alreadPaired = 1;
break;
}
}
if (alreadPaired == 0) {
if (i < v->pair[i]) {
pair->data[pairI].first = i;
pair->data[pairI].second= v->pair[i];
} else {
pair->data[pairI].first = v->pair[i];
pair->data[pairI].second= i;
}
pairI++;
}
}
}
for (int i = 0; i < fn->qty; i++) {
if (v->pair[i] < 0) {
pair->data[pairI].first = i;
pair->data[pairI].second= -1;
pairI++;
}
}
alder_seqid_file_t *v2 = malloc(sizeof(alder_seqid_file_t));
v2->filename = bstrVectorCreate(numberOfFile);
v2->type = malloc(numberOfFile * sizeof(int));
v2->format = malloc(numberOfFile * sizeof(int));
v2->pair = malloc(numberOfFile * sizeof(int));
int seqidIndex = 0;
for (int i = 0; i < pairI; i++) {
int first = pair->data[i].first;
int second = pair->data[i].second;
assert(first >= 0);
bstrVectorAdd(v2->filename, bdata(fn->entry[first]));
v2->type[seqidIndex] = v->type[first];
v2->format[seqidIndex] = v->format[first];
if (second >= 0) {
v2->pair[seqidIndex] = seqidIndex + 1;
} else {
v2->pair[seqidIndex] = -1;
}
seqidIndex++;
if (second >= 0) {
bstrVectorAdd(v2->filename, bdata(fn->entry[second]));
v2->type[seqidIndex] = v->type[second];
v2->format[seqidIndex] = v->format[second];
v2->pair[seqidIndex] = seqidIndex - 1;
seqidIndex++;
}
}
assert(seqidIndex == numberOfFile);
#if 0
for (int i = 0; i < fn->qty; i++) {
int j = v->pair[i];
if (j < 0) {
fprintf(stdout, "%2d %10s: %10s (%d) - no pair (%d)\n", i,
bdata(fn->entry[i]),
bdata(bnames->entry[i]), pairCount[i], j);
} else {
fprintf(stdout, "%2d %10s: %10s (%d) - pair %10s (%d)\n", i,
bdata(fn->entry[i]),
bdata(bnames->entry[i]), pairCount[i], bdata(fn->entry[j]), j);
}
}
fprintf(stdout, "\n");
for (int i = 0; i < fn->qty; i++) {
fprintf(stdout, "%2d %10s: format (%d), type (%d), pair (%d)\n", i,
bdata(v2->filename->entry[i]),
v2->format[i], v2->type[i], v2->pair[i]);
}
#endif
alder_seqid_file_free(v);
alder_vector_pair_t_free(pair);
bstrVectorDelete(bnames);
return v2;
}
