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| author | Roel Janssen | 2016-02-24 12:50:24 +0100 |
|---|---|---|
| committer | Roel Janssen | 2016-02-24 12:50:24 +0100 |
| commit | 1f1521af21ccdad98ad60d3d7e60c0ba4f5eb1dd (patch) | |
| tree | e4e3e7ada83ffbf862c7dcb50100fd295a0acf99 /htslib-add-cram_to_bam.patch | |
| parent | 91f6f758f40f3eeba656aa5fb7e9c1f67d38978f (diff) | |
| download | guix-bioinformatics-1f1521af21ccdad98ad60d3d7e60c0ba4f5eb1dd.tar.gz | |
A working version for Sambamba.
Diffstat (limited to 'htslib-add-cram_to_bam.patch')
| -rw-r--r-- | htslib-add-cram_to_bam.patch | 27 |
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..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 + } |