void test_seq_nonacgt(){
seq_t S;
seq_init( &S, "11ACGTNN7682394689NNTGCA11", "name");
seq_subject_init( &S);
g_assert_cmpstr(S.S, ==, "ACGTTGCA");
g_assert_cmpuint(S.len, ==, 8 );
g_assert( FLAGS & F_NON_ACGT);
g_assert_cmpstr(S.RS, ==, "TGCAACGT#ACGTTGCA");
g_assert_cmpuint(S.RSlen, ==, 8*2+1);
g_assert( S.gc == 0.5);
seq_free( &S);
FLAGS = F_NONE;
seq_init( &S, "@ACGT_!0TGCA ", "name");
seq_subject_init( &S);
g_assert_cmpstr(S.S, ==, "ACGT!TGCA");
g_assert_cmpuint(S.len, ==, 9 );
g_assert( FLAGS & F_NON_ACGT);
g_assert_cmpstr(S.RS, ==, "TGCA;ACGT#ACGT!TGCA");
g_assert_cmpuint(S.RSlen, ==, 9*2+1);
seq_free( &S);
FLAGS = F_NONE;
}
void test_seq_full(){
seq_t S;
seq_init( &S, "ACGTTGCA", "name");
int check = seq_subject_init( &S);
g_assert_cmpint(check, ==, 0);
g_assert_cmpstr(S.RS, ==, "TGCAACGT#ACGTTGCA");
g_assert_cmpuint(S.RSlen, ==, 8*2+1);
g_assert( S.gc == 0.5);
seq_free( &S);
}
/**
* @param sequences - An array of pointers to the sequences.
* @param n - The number of sequences.
*/
void run(seq_t *sequences, size_t n) {
seq_t *subject = &sequences[0];
esa_s E;
if (seq_subject_init(subject) || esa_init(&E, subject)) {
errx(1, "Failed to create index for %s.", subject->name);
}
size_t i = 0;
// now compare every other sequence to the subject
for (size_t j = 0; j < n; j++) {
if (j == i) {
continue;
}
// TODO: Provide a nicer progress indicator.
if (FLAGS & F_EXTRA_VERBOSE) {
#pragma omp critical
{ fprintf(stderr, "comparing %zu and %zu\n", i, j); }
}
size_t ql = sequences[j].len;
if (FLAGS & F_FORWARD) {
printf("> %s\n", sequences[j].name);
dist_anchor(&E, sequences[j].S, ql, subject->gc);
}
if (FLAGS & F_REVCOMP) {
char *R = revcomp(sequences[j].S, ql);
printf("> %s Reverse\n", sequences[j].name);
dist_anchor(&E, R, ql, subject->gc);
free(R);
}
}
esa_free(&E);
seq_subject_free(subject);
}
