On Mon, Dec 07, 2015 at 09:57:10PM -0800, Afif Elghraoui wrote:
>
> This error appears like you're somehow using an old version of pysam
> because AlignmentFile was introduced in 0.8.1. Are you sure you're not
> accidentally building with a Jessie chroot (where pysam is at version
> 0.7.7) rather
Hi, Andreas,
على الإثنين 7 كانون الأول 2015 01:10، كتب Andreas Tille:
>
> Hmmm, I have seen commit 7c93b9c0d42c415ef3296e6ee4a7d61b6fc34cb8 but I
> remain with failures even on amd64. :-(
>
>
> ...
> File "../doc/tss.rst", line 211, in tss.rst
> Failed example:
> for almnt in sortedbamfil
Hi Afif,
On Sun, Dec 06, 2015 at 01:41:43PM -0800, Afif Elghraoui wrote:
> > I sent an email around the same time as yours announcing the patch is in
> > git. I didn't realize this was the central issue of the bug report. If
> > that's the case, I think you should just add the "Closes..." statemen
على الأحد 6 كانون الأول 2015 13:21، كتب Afif Elghraoui:
>>> The recent pysam release dropped support for some deprecated interfaces
>>> >> and this package appears to have been affected. I can prepare a patch
>>> >> for those pysam issues as I did for pbcore [1]
>> >
>> > A patch would be cool
Hi, Andreas,
على الأحد 6 كانون الأول 2015 13:11، كتب Andreas Tille:
>>> Any idea how to fix this. Htslib upstream is unresponsive even to less
>>> hard issues.
>>>
I was confused that you were referring to this package as Htslib (I
think you also did so in your message to upstream)-- you mean
على الأحد 6 كانون الأول 2015 11:35، كتب Afif Elghraoui:
> The recent pysam release dropped support for some deprecated interfaces
> and this package appears to have been affected. I can prepare a patch
> for those pysam issues as I did for pbcore
That patch is now in git. The tests are passing o
Hi Afif,
On Sun, Dec 06, 2015 at 11:35:09AM -0800, Afif Elghraoui wrote:
> > NameError: name 'start_in_window' is not defined
>
> [...]
> >
> > Any idea how to fix this. Htslib upstream is unresponsive even to less
> > hard issues.
> >
>
> The recent pysam release dropped support for some
Hi, Andreas,
على السبت 5 كانون الأول 2015 23:53، كتب Andreas Tille:
> Hi,
>
> other uploaders of pysam in CC: When building htseq with current pysam
> in unstable I get:
>
[...]
> File
> "/build/htseq-0.6.1p1/build/lib.linux-x86_64-2.7/HTSeq/__init__.py", line
> 976, in __getitem__
>
Hi,
other uploaders of pysam in CC: When building htseq with current pysam
in unstable I get:
...
All 26 tests passed.
Doctest of tss.rst:
**
File "../doc/tss.rst", line 211, in tss.rst
Failed example:
for almnt in sortedbam
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