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- 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
- }
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