need better diagnostic output for malformed bam

[rbuels]

On 01/03/2014 05:47 AM, Keiran Raine wrote:

Hi Robert,

I've discovered after much digging that one of the tools we are using
generates uncompressed BAM files by default. Although I'm going to
correct them it's probably a good idea to:

• Update the error message to something to help diagnose the problem:
  o currently: 'ReferenceError: end is not defined'.
• Add support with warning to console that data is uncompressed.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2@sanger.ac.uk mailto:kr2@sanger.ac.uk
Tel:+44 (0)1223 834244 Ext: 7703
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[rbuels]

Hi Keiran,

I just did some testing on the volvox example bam file like:

gunzip -c volvox-sorted.bam > foo
mv foo volvox-sorted.bam

And the error message that JBrowse gives on that is "Not a BAM file", which I think is kind of reasonable.

Do you have a sample of your uncompressed BAM output (with a .bai) that I can try to reproduce this with?

[rbuels]

On 01/06/2014 11:04 AM, Keiran Raine wrote:

samtools view -u compress.bam > uncompressed.bam.

Exceptionally sparse data but this coord will give you some data: Y:9990200.