From 1f1521af21ccdad98ad60d3d7e60c0ba4f5eb1dd Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 24 Feb 2016 12:50:24 +0100
Subject: A working version for Sambamba.

---
 htslib-add-cram_to_bam.patch | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)
 create mode 100644 htslib-add-cram_to_bam.patch

(limited to 'htslib-add-cram_to_bam.patch')

diff --git a/htslib-add-cram_to_bam.patch b/htslib-add-cram_to_bam.patch
new file mode 100644
index 0000000..8c43497
--- /dev/null
+++ b/htslib-add-cram_to_bam.patch
@@ -0,0 +1,27 @@
+This patch adds the cram_to_bam function to the public interface of htslib,
+because it is used by code in Sambamba.
+
+by Roel Janssen <roel@gnu.org>
+--- a/cram/cram_decode.c	2015-12-15 17:34:33.000000000 +0100
++++ b/cram/cram_decode.c	2016-02-24 11:16:10.491808702 +0100
+@@ -2730,7 +2730,7 @@
+  * Returns the used size of the bam record on success
+  *         -1 on failure.
+  */
+-static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
++int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
+ 		       cram_record *cr, int rec, bam_seq_t **bam) {
+     int bam_idx, rg_len;
+     char name_a[1024], *name;
+diff -Naur htslib-1.3/cram/cram_decode.h htslib-1.3-patched/cram/cram_decode.h
+--- htslib-1.3/cram/cram_decode.h	2015-12-15 17:34:33.000000000 +0100
++++ htslib-1.3-patched/cram/cram_decode.h	2016-02-24 11:15:04.556809864 +0100
+@@ -104,6 +104,8 @@
+ int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
+ 		      SAM_hdr *hdr);
+ 
++int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
++                cram_record *cr, int rec, bam_seq_t **bam);
+ 
+ #ifdef __cplusplus
+ }
-- 
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