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 +--- 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 + } -- cgit v1.2.3 From c594b866b37fc38d33a87395ca8b1ef7615e2702 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 24 Feb 2016 12:53:01 +0100 Subject: Cleaner patch file. --- htslib-add-cram_to_bam.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'htslib-add-cram_to_bam.patch') diff --git a/htslib-add-cram_to_bam.patch b/htslib-add-cram_to_bam.patch index 8c43497..c90f7aa 100644 --- a/htslib-add-cram_to_bam.patch +++ b/htslib-add-cram_to_bam.patch @@ -14,8 +14,8 @@ by Roel Janssen 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 +--- 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); -- cgit v1.2.3