[med-svn] [htslib] 09/10: Stop threaded bgzf_read_block from using stale values at EOF

[Andreas Tille]

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tille pushed a commit to annotated tag 1.5
in repository htslib.

commit fba943d63bd06b5691b720253f65b6cf6673b23f
Author: Rob Davies <rmd+git at sanger.ac.uk>
Date:   Tue Jun 20 09:41:38 2017 +0100

    Stop threaded bgzf_read_block from using stale values at EOF
    
    j->block_address is not filled out at EOF, so should
    not be used.  Also initialize comp_len to zero, in
    sace anything tries to use that.
    
    Fixes samtools/samtools#687 (samtools 1.4.1 bai indices created
    with multiple threads can lose reads)
---
 bgzf.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/bgzf.c b/bgzf.c
index c8a53db..7e80b8c 100644
--- a/bgzf.c
+++ b/bgzf.c
@@ -644,7 +644,7 @@ int bgzf_read_block(BGZF *fp)
 
         // block_length=0 and block_offset set by bgzf_seek.
         if (fp->block_length != 0) fp->block_offset = 0;
-        fp->block_address = j->block_address;
+        if (!j->hit_eof) fp->block_address = j->block_address;
         fp->block_clength = j->comp_len;
         fp->block_length = j->uncomp_len;
         // bgzf_read() can change fp->block_length
@@ -1088,6 +1088,7 @@ restart:
     bgzf_job *j = pool_alloc(mt->job_pool);
     pthread_mutex_unlock(&mt->job_pool_m);
     j->errcode = 0;
+    j->comp_len = 0;
     j->uncomp_len = 0;
     j->hit_eof = 0;
 
@@ -1123,6 +1124,7 @@ restart:
         j = pool_alloc(mt->job_pool);
         pthread_mutex_unlock(&mt->job_pool_m);
         j->errcode = 0;
+        j->comp_len = 0;
         j->uncomp_len = 0;
         j->hit_eof = 0;
     }

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