[med-svn] [htslib] 09/13: Force detached read-pairs if they span references.

[Andreas Tille]

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tille pushed a commit to branch master
in repository htslib.

commit c789bed77a5f8df158351041483c98c4a0cd13ab
Author: James Bonfield <jkb at sanger.ac.uk>
Date:   Wed Jan 27 11:19:55 2016 +0000

    Force detached read-pairs if they span references.
    
    Previously it was possible for a read-pair aligned to different
    references to still be claimed as an attached-pair if they were in the
    same slice and their 5' to 3' size was as listed in their (broken?)
    tlen fields.
---
 cram/cram_encode.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 183c4ab..80b6805 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -2860,6 +2860,9 @@ static int process_one_read(cram_fd *fd, cram_container *c,
 
 
 	    // p vs this: tlen, matepos, flags
+	    if (p->ref_id != cr->ref_id)
+		goto detached;
+
 	    if (p->tlen != -sign*(aright-aleft+1))
 		goto detached;
 

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