From ce12fe7ab81aa860a6c1131b2d417e4de627a9f0 Mon Sep 17 00:00:00 2001
From: kojix2 <2xijok@gmail.com>
Date: Fri, 13 Sep 2024 12:55:03 +0900
Subject: [PATCH] Add methods in cram [wip]

---
 lib/hts/libhts/cram.rb | 43 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/lib/hts/libhts/cram.rb b/lib/hts/libhts/cram.rb
index 10a61e97..af6bb43b 100644
--- a/lib/hts/libhts/cram.rb
+++ b/lib/hts/libhts/cram.rb
@@ -89,12 +89,17 @@ module LibHTS
       [:cram_container],
       :int32
 
+    # Returns true if the container is empty (EOF marker)
     attach_function \
       :cram_container_is_empty,
       [:cram_fd],
       :int
 
-    # cram_block
+    # Returns chromosome and start/span from container struct
+    attach_function \
+      :cram_container_get_coords,
+      %i[cram_container pointer pointer],
+      :void
 
     attach_function \
       :cram_block_get_content_id,
@@ -131,6 +136,11 @@ module LibHTS
       [:cram_block],
       CramBlockMethod
 
+    attach_function \
+      :cram_expand_method,
+      [:pointer, :int32, CramBlockMethod],
+      :pointer
+
     attach_function \
       :cram_block_set_content_id,
       %i[cram_block int32],
@@ -182,6 +192,18 @@ module LibHTS
       [:cram_block],
       :uint32
 
+    # Returns the Block Content ID values referred to by a cram_codec in ids[2].
+    attach_function \
+      :cram_codec_get_content_ids,
+      [:pointer, :pointer],
+      :void
+
+    # Produces a human readable description of the codec parameters.
+    attach_function \
+      :cram_codec_describe,
+      [:pointer, KString.ptr],
+      :int
+
     # Renumbers RG numbers in a cram compression header.
     attach_function \
       :cram_transcode_rg,
@@ -195,6 +217,25 @@ module LibHTS
       %i[cram_fd cram_fd int32],
       :int
 
+    # Copies a container, but filtering it down to a specific region (as
+    # already specified in 'in'
+    attach_function \
+      :cram_filter_container,
+      %i[cram_fd cram_fd cram_container pointer],
+      :int
+
+    # Decodes a CRAM block compression header.
+    attach_function \
+      :cram_decode_compression_header,
+      %i[cram_fd cram_block],
+      :pointer # cram_block_compression_hdr
+
+    # Frees a cram_block_compression_hdr structure.
+    attach_function \
+      :cram_free_compression_header,
+      [:pointer],
+      :void
+
     # Returns the number of cram blocks within this slice.
     attach_function \
       :cram_slice_hdr_get_num_blocks,