pileup() seems broken.

[GoogleCodeExporter]

What steps will reproduce the problem?
1.

In[1]: pysam.Samfile('na12878.chr20.bam').fetch().next().pos
Out[1]: 5000001

In[2]: pysam.Samfile('na12878.chr20.bam').pileup().next().pos
Out[2]: 5000722

In[3]: pysam.Samfile('na12878.chr20.bam').pileup(stepper='samtools').next().pos
Out[3]: 5001063

What is the expected output? What do you see instead?
The starting read position should all be the same. 

What version of the product are you using? On what operating system?
pysam 0.74, Python 2.7.

Please provide any additional information below.
This is on a standard dataset which I have subsetted to the region 
chr20:5000000-10000000. 

Original issue reported on code.google.com by terho...@gmail.com on 29 Apr 2013 at 11:05

[GoogleCodeExporter]

Thanks. It seems to work when I test it.

Is it possible to make the test data available?

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 26 Jun 2013 at 8:50

• Changed state: Accepted

[GoogleCodeExporter]

Can't replicate.

Closed.

Original comment by andreas....@gmail.com on 18 Sep 2013 at 7:13

• Changed state: WontFix