Expose a bit more of the CRAM API.

This is to enable samtools cram2ref.

cram/cram_external.c

@@ -188,6 +188,19 @@ int32_t cram_slice_hdr_get_num_blocks(cram_block_slice_hdr *hdr) {
     return hdr->num_blocks;
 }
 
+int cram_slice_hdr_get_embed_ref_id(cram_block_slice_hdr *h) {
+    return h->ref_base_id;
+}
+
+void cram_slice_hdr_get_coords(cram_block_slice_hdr *h,
+                               int *refid, int *start, int *span) {
+    if (refid)
+        *refid = h->ref_seq_id;
+    if (start)
+        *start = h->ref_seq_start;
+    if (span)
+        *span  = h->ref_seq_span;
+}
 
 /*
  *-----------------------------------------------------------------------------

htslib/cram.h

@@ -247,6 +247,46 @@ int cram_transcode_rg(cram_fd *in, cram_fd *out,
 HTSLIB_EXPORT
 int cram_copy_slice(cram_fd *in, cram_fd *out, int32_t num_slice);
 
+/*
+ *-----------------------------------------------------------------------------
+ * cram slice interrogation
+ */
+
+/*
+ * Returns the number of cram blocks within this slice.
+ */
+HTSLIB_EXPORT
+int32_t cram_slice_hdr_get_num_blocks(cram_block_slice_hdr *hdr);
+
+/*
+ * Returns the block content_id for the block containing an embedded reference
+ * sequence.  If none is present, -1 is returned.
+ */
+HTSLIB_EXPORT
+int cram_slice_hdr_get_embed_ref_id(cram_block_slice_hdr *h);
+
+/*
+ * Returns slice reference ID, start and span (length) coordinates.
+ * Return parameters may be NULL in which case they are ignored.
+ */
+HTSLIB_EXPORT
+void cram_slice_hdr_get_coords(cram_block_slice_hdr *h,
+                               int *refid, int *start, int *span);
+
+/*
+ * Decodes a slice header from a cram block.
+ * Returns the opaque cram_block_slice_hdr pointer on success,
+ *         NULL on failure.
+ */
+HTSLIB_EXPORT
+cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
+
+/*
+ * Frees a cram_block_slice_hdr structure.
+ */
+HTSLIB_EXPORT
+void cram_free_slice_header(cram_block_slice_hdr *hdr);
+
 /*
  *-----------------------------------------------------------------------------
  * cram_io basics