Idx

docs/slow5_api/low_level_api/slow5_idx_load_with.md

@@ -1,15 +1,13 @@
 # slow5_idx_load_with
 
 ## NAME
-slow5_idx_load_with - loads the index file for a SLOW5 file given a file path for the index
+slow5_idx_load_with - loads the index file for a SLOW5 file for a user specified file path for the index
 
 ## SYNOPSYS
-`int slow5_idx_load_with(slow5_with_file_t *s5p, const char *pathname)`
+`int slow5_idx_load_with(slow5_file_t *s5p, const char *pathname)`
 
 ## DESCRIPTION
-`slow5_idx_load_with()` loads an index file for a SLOW5 file pointed by *s5p* into the memory from the disk and associates the index with *s5p*. If the index file is not found, the index is first created and written to the disk.
-
-`slow5_idx_load_with()` could be called instead of `slow5_idx_load_with()` when the index file is at a custom location.
+`slow5_idx_load_with()` loads an index file located at *pathname* for a SLOW5 file pointed by *s5p* into the memory from the disk and associates the index with *s5p*. If the index file is not found, it will error out.
 
 ## RETURN VALUE
 Upon successful completion, `slow5_idx_load_with()` returns a non-negative integer. Otherwise, a negative value is returned.

docs/slow5_api/slow5_internal.md

@@ -40,6 +40,9 @@ DO NOT USE.
 * slow5_hdr_set
 * slow5_hdr_add_rg_data
 
+* slow5_idx_init_empty (used in slow5curl)
+* slow5_idx_read (used in slow5curl)
+
 <!--
 int slow5_hdr_fwrite(FILE *fp, struct slow5_hdr *header, enum slow5_fmt format, slow5_press_method_t comp)
 int slow5_rec_fwrite(FILE *fp, struct slow5_rec *read, struct slow5_aux_meta *aux_meta, enum slow5_fmt format, struct slow5_press *compress)

include/slow5/slow5_mt.h

@@ -55,6 +55,7 @@ slow5_batch_t* slow5_init_batch(int batch_capacity);
 int slow5_get_next_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, int batch_size);
 int slow5_get_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, char **rid, int num_rid);
 int slow5_write_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, int batch_size);
+int slow5_encode_batch(slow5_mt_t *core, slow5_batch_t *db, int batch_size);
 void slow5_free_batch(slow5_batch_t *read_batch);
 void slow5_free_mt(slow5_mt_t *mt);
 

src/slow5_idx.c

@@ -14,11 +14,11 @@ extern enum slow5_exit_condition_opt  slow5_exit_condition;
 #define BUF_INIT_CAP (20*1024*1024)
 #define SLOW5_INDEX_BUF_INIT_CAP (64) // 2^6 TODO is this too little?
 
-static inline struct slow5_idx *slow5_idx_init_empty(void);
+
 static int slow5_idx_build(struct slow5_idx *index, struct slow5_file *s5p);
-static int slow5_idx_read(struct slow5_idx *index);
+int slow5_idx_read(struct slow5_idx *index);
 
-static inline struct slow5_idx *slow5_idx_init_empty(void) {
+struct slow5_idx *slow5_idx_init_empty(void) {
 
     struct slow5_idx *index = (struct slow5_idx *) calloc(1, sizeof *index);
     if(!index){
@@ -31,17 +31,23 @@ static inline struct slow5_idx *slow5_idx_init_empty(void) {
     return index;
 }
 
-static inline int slow5_idx_load_fp(struct slow5_idx *index, struct slow5_file *s5p, FILE *index_fp) {
+static inline int slow5_idx_load_fp(struct slow5_idx *index, struct slow5_file *s5p, FILE *index_fp, int8_t check_ts) {
 
     index->fp = index_fp;
-    int err;
-    if (slow5_filestamps_cmp(index->pathname, s5p->meta.pathname, &err) < 0.0) {
-        SLOW5_WARNING("Index file '%s' is older than slow5 file '%s'.",
-                index->pathname, s5p->meta.pathname);
-    }
-    if (err == -1) {
-        return -1;
+
+    if(check_ts){
+        int err;
+        if (slow5_filestamps_cmp(index->pathname, s5p->meta.pathname, &err) < 0.0) {
+            SLOW5_WARNING("Index file '%s' is older than slow5 file '%s'.",
+                    index->pathname, s5p->meta.pathname);
+        }
+        if (err == -1) {
+            return -1;
+        }
+    } else {
+        SLOW5_INFO("Custom index file '%s' is being used. Time stamps not checked.", index->pathname);
     }
+
     if (slow5_idx_read(index) != 0) {
         return -1;
     }
@@ -79,7 +85,7 @@ struct slow5_idx *slow5_idx_init_with(struct slow5_file *s5p, const char *pathna
         slow5_idx_free(index);
         return NULL;
     } else {
-        if (slow5_idx_load_fp(index, s5p, index_fp) != 0) {
+        if (slow5_idx_load_fp(index, s5p, index_fp, 0) != 0) {
             slow5_idx_free(index);
             return NULL;
         }
@@ -127,7 +133,7 @@ struct slow5_idx *slow5_idx_init(struct slow5_file *s5p) {
         fclose(index->fp);
         index->fp = NULL;
     } else {
-        if (slow5_idx_load_fp(index, s5p, index_fp) != 0) {
+        if (slow5_idx_load_fp(index, s5p, index_fp, 1) != 0) {
             slow5_idx_free(index);
             return NULL;
         }
@@ -398,7 +404,7 @@ int slow5_idx_write(struct slow5_idx *index, struct slow5_version version) {
     return 0;
 }
 
-static int slow5_idx_read(struct slow5_idx *index) {
+int slow5_idx_read(struct slow5_idx *index) {
 
     struct slow5_version max_supported = SLOW5_VERSION_ARRAY;
     const char magic[] = SLOW5_INDEX_MAGIC_NUMBER;

src/slow5_idx.h

@@ -47,6 +47,8 @@ struct slow5_idx {
 
 struct slow5_idx *slow5_idx_init(struct slow5_file *s5p);
 struct slow5_idx *slow5_idx_init_with(struct slow5_file *s5p, const char *pathname);
+struct slow5_idx *slow5_idx_init_empty(void);
+int slow5_idx_read(struct slow5_idx *index);
 
 /**
  * Create the index file for slow5 file.

src/slow5_mt.c

@@ -361,6 +361,11 @@ int slow5_get_next_batch(slow5_mt_t *core, slow5_batch_t *db, int batch_size){
     return num_read;
 }
 
+int slow5_encode_batch(slow5_mt_t *core, slow5_batch_t *db, int batch_size){
+    db->n_rec = batch_size;
+    slow5_work_db(core,db,slow5_work_per_single_read3);
+    return db->n_rec;
+}
 
 int slow5_write_batch(slow5_mt_t *core, slow5_batch_t *db, int batch_size){
 
@@ -501,6 +506,10 @@ int slow5_get_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, char **rid, int n
     fprintf(stderr,"slow5lib has not been compiled with lazy multithreading support\n");
     exit(EXIT_FAILURE);
 }
+int slow5_encode_batch(slow5_mt_t *core, slow5_batch_t *db, int batch_size){
+    fprintf(stderr,"slow5lib has not been compiled with lazy multithreading support\n");
+    exit(EXIT_FAILURE);
+}
 int slow5_write_batch(slow5_mt_t *mt, slow5_batch_t *read_batch, int batch_size){
     fprintf(stderr,"slow5lib has not been compiled with lazy multithreading support\n");
     exit(EXIT_FAILURE);