Re: [maq-help] missing zlib.h ?

[Heng Li <lh...@gm...>]

Hello Olivier,

Thanks a lot for your stat. It is surprising to me that Maq is faster  
than Eland. In general, I know Maq is several times slower than Eland  
because Maq has done additional stuffs like being aware of base  
qualities, using long reads and calculating mapping qualities, which  
add computational overhead. Eland should be faster. Also note that  
the latest SolexaPipeline-beta, which is now under intensive test, is  
also able to calculate more information like mapping qualities. I am  
not sure whether the whole alignment pipeline is faster than Maq.

As for the depth in "maq assemble", the hard limit on depth is 255.  
Depth higher than that will be truncated. However, the consensus is  
calculated based on all reads, not just 255 reads. You can be assured  
that all the reads are used in calling SNPs. If you want to see the  
un-truncated depth, you should try "maq pileup".

Many thanks,

Heng

On 22 Nov 2007, at 21:58, Olivier Harismendy wrote:

> Hi Heng,
>
> Thank you for your quick reply. Sorry if my question sounded a bit  
> silly but I am more like a biologist doing some computing... Zlib  
> wasn't installed on the machine I wanted to use but I had  
> everything on my iMac (Intel core duo 2.8Ghz - 4G RAM) so installed  
> it locally realized how fast your program is ! Not sure why it  
> overruns ELAND that much but this is great. Probably due to the  
> fact that you use binary files.
>
> I have another question regarding max depth. I know, through ELAND  
> that most of my depth should be higher than 300, however Maq, and  
> especially the output of cns2snp and cns2view shows a max read  
> depth of 255 : is it because of the type variable you use to  
> calculate the depth ?
>
> Thanks for your answer, I'll post this last question on the mailing  
> list as well
>
> Best
>
> Olivier
>
>
> On Nov 22, 2007, at 1:03 AM, Heng Li wrote:
>
>> Hello Olivier,
>>
>> Thanks for the feedback. You should first install zlib library  
>> (see also: http://www.zlib.net/) in your system. Zlib is a  
>> compression library distributed with most operating systems by  
>> default.
>>
>> regards,
>>
>> Heng
>>
>>
>> On 21 Nov 2007, at 20:20, Olivier Harismendy wrote:
>>
>>> Hi,
>>>
>>> I am just trying to install Maq (maq-0.6.1.tar.bz2 ) on our Linux  
>>> box and right after the ./configure I notice the zlib.h is missing.
>>>
>>> checking for stdint.h... yes
>>> checking for unistd.h... yes
>>> checking zlib.h usability... no
>>> checking zlib.h presence... no
>>> checking for zlib.h... no
>>> configure: creating ./config.status
>>> config.status: creating Makefile
>>> config.status: creating config.h
>>> config.status: config.h is unchanged
>>>
>>> I suspect this is the reason why the following make aborts.
>>>
>>> make  all-am
>>> make[1]: Entering directory `/home/oharis/Maq/maq-0.6.1'
>>> gcc -DHAVE_CONFIG_H -I. -I. -I.     -g -O2 -Wall -m64 -c `test -f  
>>> 'bfa.c' || echo './'`bfa.c
>>> bfa.c:1:18: zlib.h: No such file or directory
>>> make[1]: *** [bfa.o] Error 1
>>> make[1]: Leaving directory `/home/oharis/Maq/maq-0.6.1'
>>> make: *** [all] Error 2
>>>
>>> Do you have any idea If i am missing some piece here ?
>>>
>>> Thanks for your help
>>>
>>> Olivier
>>>
>>>
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>