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authorPjotr Prins2016-02-25 11:59:32 +0100
committerPjotr Prins2016-02-25 11:59:32 +0100
commit99eaee3ee57ab8ba6ef8d333778c472c0ab61cc6 (patch)
treef549552f2081180b68d11492a9dda30d765c801f /htslib-add-cram_to_bam.patch
parent609d1a24c9700b8de72ddba4d5b8f091e4bd0828 (diff)
parentc594b866b37fc38d33a87395ca8b1ef7615e2702 (diff)
downloadguix-bioinformatics-99eaee3ee57ab8ba6ef8d333778c472c0ab61cc6.tar.gz
Merge pull request #5 from roelj/master
Working Sambamba package.
Diffstat (limited to 'htslib-add-cram_to_bam.patch')
-rw-r--r--htslib-add-cram_to_bam.patch27
1 files changed, 27 insertions, 0 deletions
diff --git a/htslib-add-cram_to_bam.patch b/htslib-add-cram_to_bam.patch
new file mode 100644
index 0000000..c90f7aa
--- /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
+--- a/cram/cram_decode.h 2015-12-15 17:34:33.000000000 +0100
++++ b/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
+ }