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ofanoyi / pygr

Automatically exported from code.google.com/p/pygr
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Slicing on LPO produces Bus error #84

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
What steps will reproduce the problem?
from pygr import cnestedlist, sequence
s1=sequence.Sequence('aaaa','s1')
s2=sequence.Sequence('bbbb','s2')
msa = cnestedlist.NLMSA(mode='memory')
msa[0:4]+=s1
msa[0:4]+=s2
msa.build()
msaSlice = msa[0:4]
Bus error

What is the expected output? What do you see instead?
Expect to see an NLMSASlice object created, instead a crash occurs.

Suspected related error can be obtained by calling regions() method of
NLMSASlice produced through a normal sequence slicing, e.g.
msa[s1].regions()

Original issue reported on code.google.com by alexande...@gmail.com on 2 Apr 2009 at 10:03

GoogleCodeExporter commented 8 years ago 
any query on the LPO coordinate system would have crashed.  Fixed.  Also updated
sequence.absoluteSlice() to return LPO sequence intervals as regular Python 
slice
objects.

Original comment by cjlee...@gmail.com on 5 Sep 2009 at 5:52

GoogleCodeExporter commented 8 years ago 
branch/repo/commit?

Original comment by the.good...@gmail.com on 7 Sep 2009 at 12:08

GoogleCodeExporter commented 8 years ago 
Both the fix and a test for this issue are in our main repository, in 
particular the 
fix was introduced with the following commit:

http://github.com/cjlee112/pygr/commit/34f12012647f63efde664f8cbdade8e34f28c617

Original comment by mare...@gmail.com on 8 Sep 2009 at 7:22

GoogleCodeExporter commented 8 years ago 
Works! Thanks all!

Original comment by alexande...@gmail.com on 11 Sep 2009 at 6:25