First commit

pkg/obiformats/fastseq_read.c

@@ -0,0 +1,104 @@
+#include "fastseq_read.h"
+
+
+static fast_kseq_t* _open_fast_sek(gzFile fp, int shift) {
+    fast_kseq_t* iterator;
+
+    iterator = (fast_kseq_t*)malloc(sizeof(fast_kseq_t));
+
+
+    if (iterator == NULL)
+        return NULL;
+
+    iterator->filez = fp;
+    iterator->finished = false;
+    iterator->shift = shift;
+
+    if (fp != Z_NULL) {
+        iterator->seq = kseq_init(fp);
+
+        if (iterator->seq == NULL) {
+            free(iterator);
+            iterator=NULL;
+        }
+    }
+    else {
+        free(iterator);
+        iterator=NULL;
+    }
+
+    return iterator;
+}
+
+/**
+ * @brief open a FastA or FastQ file gizzed or not 
+ * 
+ * @param filename a const char* indicating the path of the 
+ *        fast* file
+ * @return kseq_t* a pointer to a kseq_t structure or NULL on
+ *         failing
+ */
+fast_kseq_t* open_fast_sek_file(const char* filename, int shift) {
+    gzFile fp;  
+
+    fp = gzopen(filename, "r");  
+    return _open_fast_sek(fp, shift);
+}
+
+fast_kseq_p open_fast_sek_fd(int fd, bool keep_open, int shift) {
+    gzFile fp;  
+
+    if (keep_open)
+        fd = dup(fd);
+
+    fp = gzdopen(fd, "r"); 
+    return _open_fast_sek(fp, shift);
+}
+
+fast_kseq_p open_fast_sek_stdin(int shift) {
+    return open_fast_sek_fd(fileno(stdin), true, shift);
+}
+
+
+int64_t next_fast_sek(fast_kseq_t* iterator) {
+    int64_t l;
+
+    if (iterator == NULL || iterator->seq == NULL)
+        return -3;
+
+    l = kseq_read(iterator->seq);
+    iterator->finished = l==0;
+    if (l>0) l = gzoffset(iterator->filez);
+    return l;
+}
+
+int rewind_fast_sek(fast_kseq_t* iterator) {
+    if (iterator == NULL || iterator->seq == NULL)
+        return -3;
+
+    kseq_rewind(iterator->seq);
+    return 0;
+}
+
+int close_fast_sek(fast_kseq_t* iterator) {
+    gzFile fp;  
+    kseq_t *seq;
+    int rep = -3;
+
+    if (iterator == NULL)
+        return rep;
+
+    fp  = iterator->filez;
+    seq = iterator->seq;
+
+    free(iterator);
+
+    if (seq != NULL)
+        kseq_destroy(iterator->seq);
+
+    if (fp != Z_NULL)
+        rep = gzclose(fp);
+
+    return rep;
+}
+