#73 tg_index fails to process BAM files in staden-2.0.0b6-x86_64

open
Gap5 (15)
5
2010-05-21
2010-05-20
Anonymous
No

I tried to use tg_index from the staden-2.0.0b6-x86_64 binary package, and received the following error. I'm running Ubuntu 9.04 (64-bit).

Processing BAM file ../p172_400bp_trimmed.fastq.sorted.bam

++Processing contig 0 / mygapseq
New library ../p172_400bp_trimmed.fastq.sorted.bam
tg_index.bin: /nfs/users/nfs_j/jkb/staden/trunk/src/build.static/../gap5/sam_index.c:1095: bio_callback: Assertion `i == i2' failed.
Aborted

Discussion

  • James Bonfield
    James Bonfield
    2010-05-21

    Does "samtools pileup" work on the bam file too? Can you "samtools tview" the bam and scroll past the offending part that caused the abort?

    I've seen this in the past, but only with sam files which samtools cannot cope. Typically this is due to insertions and deletions next to each other in the CIGAR string. I've tried to justify this as a bug in samtools (which tg_index uses in library-form for reading bam files), but I don't believe it's been fixed yet.

    If you could trim down the bam file to something smaller, sufficient to email or attach (if public), then I'll take a look at it to see whether it's something I can cope with better. It may perhaps be preferable to issue a warning and skip corrupted data rather than aborting the entire process.

     
  • James Bonfield
    James Bonfield
    2010-05-21

    • assigned_to: nobody --> jkbonfield
     
  • James Bonfield
    James Bonfield
    2010-05-21

    • labels: --> Gap5