pysam can't find bam index

[Luke Noble]

Hello,

pysam seemed to install without complaint and works fine for me on sam files, but fails to find the matching .bai file when I try to iterate over bam files.

e.g.

File "csamtools.pyx", line 749, in csamtools.Samfile.fetch (pysam/csamtools.c:8439)

ValueError: fetch called on bamfile without index

Any ideas?

probably, sigh, system specific... I've not found any reference to this error elsewhere.

Cheers,

Luke

pysam 0.5

python 2.7

pyrex 0.9.9

cython 0.14.1 

on Mac OS X 10.7

[Readman Chiu]

Hi Luke,

You have to use Samtools sort and index your bam file before it's usable by Pysam for accessing read alignments.

cheers,
Readman

[Luke Noble]

Thanks Readman, 

But for all cases, the .bai is sitting there in the same directory as the .bam, identically named but for the extension. They're just not being recognised.

Luke

[Peter Cock]

Using example.bam do you have example.bai or
example.bam.bai as the index? Sadly samtools
and Picard picked different conventions, I'm not
sure if pysam checks both.

Peter

[Sean Davis]

You'll need a file called example.bam.bai (samtools convention) for pysam.  Either rename or softlink the .bai file and you should be set.

Sean