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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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