Re: [Samtools-help] A bug report in samtools (bgzf.cpp)

[Heng Li <lh...@sa...>]

I have never used bam_tell() with bam_write(). I only use bam_tell() with bam_read().

If bam_flush_try() is causing the problem, you may comment out that line. I am afraid that there is no easy solution to allow both bam_tell+bam_write and bam_flush_try().

Heng

On Jan 25, 2012, at 10:09 AM, Daehwan Kim wrote:

> Hi guys,
> 
> I wrote bam records (bam_write) while storing the locations of those
> records (bam_tell).  In the second step, when I opened the bam file, I
> could not retrieve some records in some case (bam_seek).
> 
> For instance, (1) bgzf_seek is called with "block offset = 65503" (or
> "offset" of 67186393055), which is very close to the size of the
> uncompressed block 65536 (or 2^16), and then followed by (2) bgzf_read,
> which failed to retrieve a bam record.
> 
> I detected this issue in a mixture of bam_write and bam_tell, for
> instance, a call to bam_tell returns the block offset of 65503, but the
> next call of bam_write writes a bam record onto the next block (as the
> new record cannot fit into the current block), so the actual location of
> the new record is the new block address and the block offset of 0, which
> is not the same as the one I got from the bam_tell function.  This is
> due to the "bgzf_flush" called in "bam_write1_core" function in bam.c.
> 
> 
> Thanks,
> Daehwan
> 
> 
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