[med-svn] [htslib] 01/01: add the cram_to_bam function to the public interface of htslib because it is used by code in Sambamba

[Andreas Tille]

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tille pushed a commit to branch debian/unstable
in repository htslib.

commit d6cab913f23c6557b430fa9a2e02a5af9f3f94a7
Author: Andreas Tille <tille at debian.org>
Date:   Thu May 4 10:57:51 2017 +0200

    add the cram_to_bam function to the public interface of htslib because it is used by code in Sambamba
---
 debian/changelog                            |  7 +++++++
 debian/patches/htslib-add-cram_to_bam.patch | 28 ++++++++++++++++++++++++++++
 debian/patches/series                       |  1 +
 3 files changed, 36 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 51c8220..94a7362 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+htslib (1.4-3) experimental; urgency=medium
+
+  * add the cram_to_bam function to the public interface of htslib because
+    it is used by code in Sambamba
+
+ -- Andreas Tille <tille at debian.org>  Thu, 04 May 2017 10:57:31 +0200
+
 htslib (1.4-2) experimental; urgency=medium
 
   * Include htsfile binary into tabix package since its used by manta
diff --git a/debian/patches/htslib-add-cram_to_bam.patch b/debian/patches/htslib-add-cram_to_bam.patch
new file mode 100644
index 0000000..7b995ba
--- /dev/null
+++ b/debian/patches/htslib-add-cram_to_bam.patch
@@ -0,0 +1,28 @@
+Description: This patch adds the cram_to_bam function to the public interface of htslib,
+ because it is used by code in Sambamba.
+Author: Roel Janssen <roel at gnu.org>
+Last-Update: 3 May 2016
+Origin: https://github.com/UMCUGenetics/guix-additions/blob/master/htslib-add-cram_to_bam.patch
+
+--- a/cram/cram_decode.c
++++ b/cram/cram_decode.c
+@@ -2821,7 +2821,7 @@ int cram_decode_slice_mt(cram_fd *fd, cr
+  * 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;
+--- a/cram/cram_decode.h
++++ b/cram/cram_decode.h
+@@ -104,6 +104,8 @@ cram_block_slice_hdr *cram_decode_slice_
+ 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
+ }
diff --git a/debian/patches/series b/debian/patches/series
index 7672d11..917bd4c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 define_PATH_MAX.patch
 literal_version.patch
 fix_pkg-config.patch
+htslib-add-cram_to_bam.patch

-- 
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