mafFileApi_t* maf_newMfa(const char *filename, char const *mode) {
mafFileApi_t *mfa = (mafFileApi_t *) de_malloc(sizeof(*mfa));
mfa->lineNumber = 0;
mfa->lastLine = NULL;
mfa->mfp = de_fopen(filename, mode);
mfa->filename = de_strdup(filename);
return mfa;
}
static void test_readingFasta_0(CuTest *testCase) {
char inputName[] = ">simChimp.chrA";
char inputSequence[] = "ATAATACTTGCACACTTCTGCTATTACTTGATGTGTTTTCTATGGGGTGT"
"CTTTCAGTGCTATGGGCAAGGCCATGGATTAATGGTGCCATAATTGCTCT"
"AGGCAGTGACTAGAAACAGTTCACAAGTTTTTACTGTATCAAACTATGTT"
"TTATAGTACGATTCACCCTCCAGGGGACCATCCCAAACTACTGGCCTAAA"
"AGGACCTGCCATGTTGTAACTCCCCAGCTTAGAAATATAGACGGGAGGAA"
"TGACaaaaagaagaaaaaaaaaaaaagaaaaaataaaaaaaaaacaaaaa"
"agatagagaaaaaaaaaagtaaaaacaaaaaaaaataaaaaagggaaaaa"
"aaataacaaaggaacaaaaaaaaaaaaaaaaaaataaaaagaaaaaCAAG"
"ATAACCTTCATGCCATTGGAGCTATCTATTATTGTCTTGACCTATGCTTT"
"ATCAATTTCTTCCTTCCTAGGAAGACATTTTTCTAGAAAGCTAAACGTTT"
"TTGTAGGCTTGCATGTTCTGTCTGGGCTTGAATGGTTGTGCGTCTACAAG"
"CCTCATTTACCATAGCACCATGCTTGGGTGGTATCTATCATCATTATCAA"
"TAGTCAAGTCATTATAATGTTTTGGTGATCAGGCCAGATCCCTTGCACCA"
"GTGACTTTCTAAATAGCACCTCCTCCATCATTTAAGGATCTCTAGCAACT"
"TTAATCTGACTCACCTTGCCATGCAGAGTGCATGTTCCTTTTTAACACCC"
"TGTGATTATGGGTTGGGTCTATTTGTATTTGTTTGATTACATCAGACGAC"
"CAGGCCAGAGACAGATAAACACAACAGCCACTGGAACCTAAAGCTGTGTT"
"CAGAATGTCACGGAATGTCTCATTGCACCCAGAGCTAGGGTGGGTATGAG"
"TATGATCTTCTACATAAGGTACCCCAGGAAAATTAACTTAACAACCAATC"
"AATTACAGAAGATGAATTCTGCTGTTGTCTCTTATTAGTTGGACTATTCA"
"GCCTAATGGTTGGCCACTTAGCTTGTCATGAGCATTACTGTACTACTATG"
"TCTAGTGTTTCCAGTTATTAGTTAGCCCACTGGATAGACAGTTTTGGCTT"
"GTTTTCTTTCATTTGTATTGCCCACTCACCTAGCAAATCAGACAAAGGGG"
"CATGTGAAAACTACCTTAGACTCTGCAGTTAGACAAACCATACTTTCCAC"
"ATAGACCTCAGACATTTGGACATGAATAATTTCCTTCCTCCGGAGTGGTG"
"GTTCCTCAACACTTATCACTTTCTTCTTCTTTTACCCGTATCACTGTCAA";
FILE *ofp = de_fopen("testFasta.fa", "w");
fprintf(ofp, "%s\n", inputName);
for (size_t i = 0; i < strlen(inputSequence); ++i) {
fprintf(ofp, "%c", inputSequence[i]);
if (((i + 1) % 50) == 0) {
fprintf(ofp, "\n");
}
}
fprintf(ofp, "\n");
fclose(ofp);
stHash *sequenceHash = stHash_construct3(stHash_stringKey, stHash_stringEqualKey, free, destroyMtfseq);
addSequencesToHash(sequenceHash, "testFasta.fa");
mtfseq_t *value = NULL;
CuAssertTrue(testCase, (value = stHash_search(sequenceHash, "not in there")) == NULL);
CuAssertTrue(testCase, (value = stHash_search(sequenceHash, "simChimp.chrA")) != NULL);
if (value != NULL) {
CuAssertTrue(testCase, strlen(value->seq) == strlen(inputSequence));
CuAssertTrue(testCase, strcmp(value->seq, inputSequence) == 0);
}
if (remove("testFasta.fa")) {
fprintf(stderr, "Error, unable to remove temporary file testFasta.fa\n");
exit(EXIT_FAILURE);
}
stHash_destruct(sequenceHash);
}
static de_file_ref_t prep_new_core_file(struct dump_s *s)
{
char name[80];
int i;
de_file_ref_t file;
for(i=1 ; i <= DE_COREDUMP_MAX_COUNT ; i++)
{
DE_SNPRINTF(name, sizeof(name), CORE_FILE_NAME, i);
file = de_fopen(name, DE_FRDONLY );
if(de_f_is_open(file))
{
de_fclose(file);
}
else
{
s->nr = i;
return de_fopen(name, DE_FCREATE|DE_FWRONLY|DE_FTRUNC);
}
}
return NULL;
}
