Thanks James,
it seems that bgzf_seek and bgzf_tell work better even if I get a crash
after about 43000 reads...
What I do now is
iPos = bgzf_tell()
some read_bam1 calls...
bgzf_seek(iPos)
Claudio
On 07/12/2015 16:33, James Bonfield wrote:
Hello Claudio,
On Mon, Dec 07, 2015 at 12:18:22PM +0100, Claudio Alberti wrote:
lOffset = hts_utell(htsInputFile);
hts_useek(htsInputFile, lOffset, SEEK_SET);
Now the problem is that after parsing a few records I get an assertion
bgzf_useek: Assertion `fp->block_offset <= fp->block_length' failed.
fp->block_offset is 66644 while block_length is 65498.
Any idea why this is happening and how to prevent it?
See also this thread:
http://sourceforge.net/p/samtools/mailman/message/34430632/
I'm less clear on the actual fix though, sorry for not realising this
earlier when I replied to you. From reading that thread it appears:
- hts_seek / hts_tell (or useek/utell) aren't supported functions.
They're not in public header files, so shouldn't be expected to work
(and indeed don't in all cases as you've seen). I'm not sure what's
missing / broken though, perhaps just the purging of the read-ahead
buffer after a seek.
- htell/hseek only work if all of your I/O is via the lower level
hFILE object. If you try to fix hts_file I/O with htell/hseek then
the buffering breaks things. (The analogy is lseek on a fileno(fp)
for FILE* and then try using fread.)
I'm not sure the solution actually exists therefore apart from rolling
your own interface or avoid using the hts_file layer and do all BAM
reading via the lower level bgzf_open/bgzf_read layer. (And similarly
with a different code path for CRAM.)
Probably not the answer you wanted.
James
--
Claudio Alberti
----------------------------------------------
http://gramm.epfl.ch
EPFL SCI STI MM
ELG 140 (ELG Building)
Station 11
CH-1015 Lausanne - Switzerland
Tel. +41 21 6936869
----------------------------------------------
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
