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 --- 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 }