diff options
| author | Pjotr Prins | 2016-02-25 11:59:32 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2016-02-25 11:59:32 +0100 |
| commit | 99eaee3ee57ab8ba6ef8d333778c472c0ab61cc6 (patch) | |
| tree | f549552f2081180b68d11492a9dda30d765c801f /htslib-add-cram_to_bam.patch | |
| parent | 609d1a24c9700b8de72ddba4d5b8f091e4bd0828 (diff) | |
| parent | c594b866b37fc38d33a87395ca8b1ef7615e2702 (diff) | |
| download | guix-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.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..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 + } |