[BioRuby] samtools-ruby

[Michal]

Hi,
I would be happy if would find out how to get on a particular position 
the alignment and then I could give feedback.

Pysam http://code.google.com/p/pysam/ contains all files and tests.
~/Downloads/pysam-0.3.1/tests$ ls
00README.txt  ex4.sam  ex8.sam             Makefile
ex1.fa        ex5.sam  example.gtf.gz      pysam_test.py
ex1.sam.gz    ex6.sam  example.gtf.gz.tbi  segfault_tests.py
ex3.sam       ex7.sam  example.py          tabix_test.py

Maybe it would be possible to test bioruby-samtools in the same way. 
Pysam is ship out with samtools source code and maybe could be used it 
for bioruby-samtools.

Thank you in advance.

Michal


On 02/04/2011 10:26 PM, Tomoaki NISHIYAMA wrote:
> Hi,
>
>> What I have forgotten to do?
>
> Now, you are at the point I reached yesterday and
> I don't think you have forgotten anything.
>
> From yesterday's mail:
>>   1) Failure:
>> test: BioSamtools should probably rename this file and start testing 
>> for real. (TestBioSamtools) [test/test_bio-samtools.rb:5]:
>> hey buddy, you should probably rename this file and start testing for 
>> real
>>
>> Loading seems ok.
>> I'm not sure if this is bad or ok.
>
> You could look at test/test_bio-samtools.rb
> $ cat test/test_bio-samtools.rb
> require 'helper'
>
> class TestBioSamtools < Test::Unit::TestCase
>   should "probably rename this file and start testing for real" do
>     flunk "hey buddy, you should probably rename this file and start 
> testing for real"
>   end
> end
>
> and guess what it means.
>
> My guess is that this is test not implemented yet.
> So, this error does not tell if the library function well or can not 
> used at all.
> You might just try what you wanted to do and see if it works.
>
>> I understand how difficult it is to keep track and it is a good idea 
>> to ship bioruby-samtools
>> with a working samtools version like Raoul does it.
>
> My view is the opposite.
> Since it potentially has many bugs and changes rapidly, bundled 
> shipping is ineffective.
> With the lack of test code, we cannot even tell which is a good 
> working version.
>
> --
>
> Tomoaki NISHIYAMA
>
>
> Advanced Science Research Center,
>
> Kanazawa University,
>
> 13-1 Takara-machi,
>
> Kanazawa, 920-0934, Japan
>
>