segmentation fault in merge

[philipp....@gmail.com]

Hi!

When running bamtools merge on two files like this

bamtools merge -in Bornheim.Bornheimx.result.ref.fna.masked.gsnap.2.global.h.bam -in B3I_UNclean_shuf.gsnap.Bornheim.Bornheimx.result.ref.noN.bam -out test.out.bam

I get the following error

bamtools merge ERROR: could not open input BAM file(s)... Aborting.

[1]    16266 segmentation fault  bamtools merge -in  -in  -out test.out.bam.

This is for the latest bamtools, as well as bamtools-2.2.3.

This happens for a bunch of bam files that have been created from gsnap mappings with samtools 0.2.0. I am able to merge other bam files created from clc mappings with the clc conversion tool.

Any help and/or workaround would be highly appreciated.

Kind regards

Philipp

[Derek Barnett]

Hi Philipp,
Not quite sure what's going on here without more info, but errors in opening files for merging usually involves the BAM files not having the same reference sequence information. Not sure if or why this would cause a segfault, but it's likely related to this.

Can you run this command on each of your files and let me know if the output differs? (I should probably make a utility that dumps this info for checking into situations like this, instead of having to read the whole file.)

    $ bamtools coverage -in <BAM> | cut -f 1 | uniq 

(NOTE: order of output matters )

Feel free to reply directly, so we don't have to spam the group with a bunch of case-specific discussion.
  - Derek

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