An update on the issue,
I was able to seek and tell the BAM file by using
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?
Claudio
On 04/12/2015 12:11, Claudio Alberti wrote:
Dear Samtools team,
I'm writing a BAM parser by integrating htslib and I need to be able
to tell and seek a BAM file to read back and forth BAM records.
I'm using bam_read1 to sequential read records but sometime I have to
go back and continue from a previous position, so I'm looking for a
tell/seek type API.
I found htell and hseek in hfile.h, but they seem to be not working
the way I expected.
I currently try this to record the cursor position and then come back
to the same record
iCurPos = htell(htsInputFile->fp.bgzf->fp)
...some bam_read1 calls....
hseek(htsInputFile->fp.bgzf->fp, iCurPos, SEEK_SET)
After the hseek call the bam_read1 calls continue reading without
going back to iCurPos.
What am I doing wrong?
Is there any other way to achieve this.
Thanks!
Kind regards,
Claudio
--
Claudio Alberti
----------------------------------------------
EPFL SCI STI MM
ELG 140 (ELG Building)
Station 11
CH-1015 Lausanne - Switzerland
Tel. +41 21 6936869
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Claudio Alberti
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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
_______________________________________________
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[email protected]
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