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27 lines
1.1 KiB
27 lines
1.1 KiB
This patch adds the cram_to_bam function to the public interface of htslib,
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because it is used by code in Sambamba.
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by Roel Janssen <roel@gnu.org>
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--- a/cram/cram_decode.c 2015-12-15 17:34:33.000000000 +0100
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+++ b/cram/cram_decode.c 2016-02-24 11:16:10.491808702 +0100
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@@ -2730,7 +2730,7 @@
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* Returns the used size of the bam record on success
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* -1 on failure.
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*/
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-static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
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+int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
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cram_record *cr, int rec, bam_seq_t **bam) {
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int bam_idx, rg_len;
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char name_a[1024], *name;
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diff -Naur htslib-1.3/cram/cram_decode.h htslib-1.3-patched/cram/cram_decode.h
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--- a/cram/cram_decode.h 2015-12-15 17:34:33.000000000 +0100
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+++ b/cram/cram_decode.h 2016-02-24 11:15:04.556809864 +0100
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@@ -104,6 +104,8 @@
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int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
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SAM_hdr *hdr);
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+int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
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+ cram_record *cr, int rec, bam_seq_t **bam);
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#ifdef __cplusplus
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}
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