until_eof parameter not exist

GoogleCodeExporter commented 9 years ago

Dear developer, 

 File "csamtools.pyx", line 597, in csamtools.Samfile.__cinit__ (pysam/csamtools.c:5982)
 File "csamtools.pyx", line 610, in csamtools.Samfile._open (pysam/csamtools.c:6313)
 TypeError: _open() got an unexpected keyword argument 'until_eof'

$ python
Python 2.7.3 (default, Aug  1 2012, 05:14:39) 
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pysam
>>> pysam.__version__
'0.7.4'
>>> 

Does this option has beeb deprecated?
Was using IteratorRowAll the only way to get unmapped reads then?
Thanks!

Original issue reported on code.google.com by lid...@gmail.com on 27 May 2013 at 5:29

GoogleCodeExporter commented 9 years ago

Also encounter following error when trying to use IteratorRowAll:

    for read in samfile.IteratorRowAll():
AttributeError: 'csamtools.Samfile' object has no attribute 'IteratorRowAll'

Thanks!

Original comment by lid...@gmail.com on 27 May 2013 at 9:16

GoogleCodeExporter commented 9 years ago

Thanks.

1. until_eof is a keyword to the fetch() method - could this be the problem?

2. IteratorRowAll is not exported - do you need direct access to it? The basic 
idea
is to call fetch() to return an iterator.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 26 Jun 2013 at 9:09

GoogleCodeExporter commented 9 years ago

I close this issue for the time being.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 17 Sep 2013 at 7:25

Changed state: Invalid

brittneybrinsfield / pysam

until_eof parameter not exist #125