fixed db error

lmdu · Aug 27, 2023 · d39bc5c · d39bc5c
1 parent 77fa52a
commit d39bc5c
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Showing 5 changed files with 13 additions and 10 deletions.
diff --git a/src/fakeys.c b/src/fakeys.c
@@ -162,7 +162,7 @@ Py_ssize_t pyfastx_fasta_keys_length(pyfastx_FastaKeys *self) {
 }
 
 PyObject *pyfastx_fasta_keys_repr(pyfastx_FastaKeys *self) {
-	return PyUnicode_FromFormat("<FastaKeys> contains %ld keys", self->seq_counts);
+	return PyUnicode_FromFormat("<FastaKeys> contains %zd keys", self->seq_counts);
 }
 
 PyObject *pyfastx_fasta_keys_subscript(pyfastx_FastaKeys *self, PyObject *item) {

diff --git a/src/fasta.c b/src/fasta.c
@@ -57,7 +57,7 @@ PyObject *pyfastx_fasta_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 	PyObject *index_obj = NULL;
 
 	//key function for seperating name
-	PyObject *key_func = Py_None;
+	PyObject *key_func = NULL;
 
 	pyfastx_Fasta *obj;
 
@@ -68,7 +68,7 @@ PyObject *pyfastx_fasta_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 		return NULL;
 	}
 
-	if ((key_func != Py_None) && !PyCallable_Check(key_func)) {
+	if ((key_func) && !PyCallable_Check(key_func)) {
 		PyErr_SetString(PyExc_TypeError, "key_func must be a callable function");
 		return NULL;
 	}
@@ -101,7 +101,7 @@ PyObject *pyfastx_fasta_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 
 	//create index
 
-	obj->index = pyfastx_init_index((PyObject *)obj, obj->file_obj, index_obj, uppercase, full_name, memory_index, key_func);
+	obj->index = pyfastx_init_index((PyObject *)obj, file_obj, index_obj, uppercase, full_name, memory_index, key_func);
 
 	//iter function
 	obj->func = pyfastx_index_next_null;
@@ -132,9 +132,8 @@ PyObject *pyfastx_fasta_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 
 void pyfastx_fasta_dealloc(pyfastx_Fasta *self){
 	//free(self->file_name);
-	Py_DECREF(self->file_obj);
-
 	pyfastx_index_free(self->index);
+	Py_DECREF(self->file_obj);
 	Py_TYPE(self)->tp_free((PyObject *)self);
 }
 

diff --git a/src/fastq.c b/src/fastq.c
@@ -408,6 +408,8 @@ void pyfastx_fastq_dealloc(pyfastx_Fastq *self) {
 	fclose(self->middle->fd);
 	gzclose(self->middle->gzfd);
 
+	Py_DECREF(self->file_obj);
+
 	Py_TYPE(self)->tp_free((PyObject *)self);
 }
 

diff --git a/src/fastx.c b/src/fastx.c
@@ -33,7 +33,6 @@ PyObject *pyfastx_fastx_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 	int uppercase = 0;
 	int comment = 0;
 
-	char *file_name;
 	char *format = "auto";
 
 	PyObject *file_obj;
@@ -108,9 +107,9 @@ PyObject *pyfastx_fastx_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 }
 
 void pyfastx_fastx_dealloc(pyfastx_Fastx *self) {
-	Py_DECREF(self->file_obj);
 	kseq_destroy(self->kseqs);
 	gzclose(self->gzfd);
+	Py_DECREF(self->file_obj);
 	Py_TYPE(self)->tp_free((PyObject *)self);
 }
 

diff --git a/src/index.c b/src/index.c
@@ -22,6 +22,9 @@ pyfastx_Index* pyfastx_init_index(PyObject *obj, PyObject* file_obj, PyObject* i
 	index->uppercase = uppercase;
 
 	//key function
+	if (key_func) {
+		Py_INCREF(key_func);
+	}
 	index->key_func = key_func;
 
 	//full name
@@ -161,7 +164,7 @@ void pyfastx_create_index(pyfastx_Index *self){
 	PYFASTX_SQLITE_CALL(ret = sqlite3_open(self->index_file, &self->index_db));
 
 	if (ret != SQLITE_OK) {
-		PyErr_Format(PyExc_ConnectionError, "Can not open index file %s", self->index_file);
+		PyErr_Format(PyExc_ConnectionError, "Could not open index file %s", self->index_file);
 		return;
 	}
 
@@ -269,7 +272,7 @@ void pyfastx_create_index(pyfastx_Index *self){
 			//remove > sign at the start position
 			header_pos = line.s + 1;
 
-			if (self->key_func == Py_None) {
+			if (self->key_func == NULL) {
 				if (self->full_name) {
 					chrom.l = desc_len;
 					memcpy(chrom.s, header_pos, chrom.l);