[ruanjue]

Please have a test. If you are running maqview on 32-bit machine, hope this new version helps.

Note: maqview-0.2.6 haven't been released in sourceforge, this package is just for test, if you find any new bug, please reply.

[lparsons]

The 0.2.6 version fixed the "Bus error" on my 64-bit Mac. Thank you for the fix and the excellent viewer. Let me know if I can help with testing, etc.

[ruanjue]

I am happy that it works fine

maqview-0.2.6 added `depth view`
<F1> basic alignment view
<F2> colored alignment view
<F3> line reads view
<F4> depths view

[lparsons]

I was able to see line reads, though I'm a bit confused as to what the color scheme for the reference and reads means.

Also, I wasn't able to see depths view. Pressing F4 seems to have no effect.

[bosTau2]

compiling errors

I compiled maqview-0.2.6 in two Linux machines, which did not have problems before. Now I got errors in 'make'.
I tried on
Linux 2.6.18-8.el5, x86_64 x86_64 x86_64 GNU/Linux
Linux 2.6.5--286tg3susesfs, x86_64 GNU/Linux

Here is a make output.

#portal maqview>make
make all-am
make[1]: Entering directory `/cluster/home/maqview2/maqview'
if gcc -DHAVE_CONFIG_H -I. -I. -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -lm -DMAQ_
LONGREADS -MT zrio_main.o -MD -MP -MF ".deps/zrio_main.Tpo" -c -o zrio_main.o zr
io_main.c; \
then mv -f ".deps/zrio_main.Tpo" ".deps/zrio_main.Po"; else rm -f ".deps
/zrio_main.Tpo"; exit 1; fi
gcc: -lm: linker input file unused because linking not done
gcc: -lm: linker input file unused because linking not done
if gcc -DHAVE_CONFIG_H -I. -I. -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -lm -DMAQ_
LONGREADS -MT btree.o -MD -MP -MF ".deps/btree.Tpo" -c -o btree.o btree.c; \
then mv -f ".deps/btree.Tpo" ".deps/btree.Po"; else rm -f ".deps/btree.T
po"; exit 1; fi
gcc: -lm: linker input file unused because linking not done
gcc: -lm: linker input file unused because linking not done
if gcc -DHAVE_CONFIG_H -I. -I. -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -lm -DMAQ_
LONGREADS -MT maqmap_index.o -MD -MP -MF ".deps/maqmap_index.Tpo" -c -o maqmap_i
ndex.o maqmap_index.c; \
then mv -f ".deps/maqmap_index.Tpo" ".deps/maqmap_index.Po"; else rm -f
".deps/maqmap_index.Tpo"; exit 1; fi
gcc: -lm: linker input file unused because linking not done
In file included from maqmap.h:28,
from maqmap_index.h:5,
from maqmap_index.c:2:
const.h:11: error: conflicting types for â
/usr/include/sys/types.h:198: error: previous declaration of â was here
maqmap_index.c: In function â:
maqmap_index.c:178: warning: passing argument 3 of â from incompatible pointer t
ype
maqmap_index.c: In function â:
maqmap_index.c:432: warning: comparison between signed and unsigned
maqmap_index.c:434: warning: format â expects type â, but argument 3 has type â
make[1]: *** [maqmap_index.o] Error 1
make[1]: Leaving directory `/cluster/home/maqview2/maqview'
make: *** [all] Error 2

[ruanjue]

Please try replace const.h:11 with those lines
#ifndef int64_t
typedef signed long long int int64_t;
#endif

[Torst]

bosTau2,

I had to edit "const.h" and comment out the int64_t typedef, as there was already a "previous declaration" in another .h file it included:

//typedef signed long long int int64_t;

That allowed compilation to succeed on my 64 bit Linux systems.

--Torst

[bosTau2]

//typedef signed long long int int64_t; fixes the problem

Thank you for both answering my questions. I tried both but
//typedef signed long long int int64_t; fixed my problem.

This is a bit different issue but related to a sequence viewer. Have any one tried ssaha_pileup/view_pileup which provide very simple alignments around a single coordinate?

I used MAQ and ssaha2 for a same data set. MAQ and maqview(0.2.5) gave me clean alignments. But ssaha_pileup/view_pileup showed me bad alignments. ssaha2 told me that 97% of the reads are aligned.

I have another question to ruanjue. How difficult is it to convert MAQ alignment format to ace or some alignment format keeping essential information? I am interested in converting ssaha2 alignment format shown below to mapview output for LookSeq (Magnus, Sanger) tools. LookSeq uses MAQ output format. I was told that I should consult with others before I try this.


Score Q_Name S_Name Q_Start Q_End S_Start S_End Direction #Bases identity
95 query subject 1 121 1 120 F 121 95.87 121

Query 1 AACTAAGCTTTCATATCTGCAAGCATCTTTGGGAATACTCTTGACATTGATT 59
v -
Sbjct 1 AACTAAGCTTTCATATCTCCAAGCATCTTTGGGAATACTCTTGACATTGATT 60

Base quality etc are available in different files.

[Albert N]

Can somebody help a desperate student?

Heeeelp!

I have some troubles triying to compile maqview-0.2.6 (sorry I'm a beginner).
Install file says: "To compile it, just run"./autogen.sh; ./configure; make"......but when I type ./autogen this is the output:
albert@mambara:~/maqview$ ./autogen.sh
running: aclocal
eval: 1: aclocal: not found
error: while running 'aclocal'

Somebody knows what am I doing wrong?

[Torst]

I have some troubles triying to compile maqview-0.2.6
albert@mambara:~/maqview$ ./autogen.sh
running: aclocal
eval: 1: aclocal: not found
error: while running 'aclocal'

You need to install the "automake" software package as the autogen.sh script needs it.

If automake is not installed, there is a good chance that none of the developer/compilation packages are installed either (eg. gcc) so you may be busy for a while!

[Albert N]

You need to install the "automake" software package as the autogen.sh script needs it.

If automake is not installed, there is a good chance that none of the developer/compilation packages are installed either (eg. gcc) so you may be busy for a while!

hi,
thanks for your reply.
It works perfectly (sudo apt-get install automake)!!!
but now it seems that I don't have the GLUT/glut.h library
As you said, I will be busy for a while

[Torst]

GLUT is the OpenGL user toolkit. The glut.h is a C header file for compiling programs which use the toolkit (like MaqView does).

As you are using apt-get I assume you have a Debian or Ubuntu system. If you go to System :: Administration :: Synaptic Packager Manager and search for "GLUT" you will see lots of glut related packages you don't have installed.

To get the glut.h file for compiling software, you will need the correct -dev package. For example, freeglut3-dev and/or libglut3-dev .

Hope that works for you.

[KiTrinet]

error

Hi everyone I have a question in regards to viewing data in maqview,
i obtained a binary file cns in maq however whenever i try to maqindex with map file i fail to do get any information

i will briefly describe the commands

first

i try to convert the old map file into new map file using

maq mapass2maq old.map new.map

than once that gets converted i use

maqindex xxx.cns new.map

however there is a segmentation failure over here

so i tried to carry it at maqview but also failed in this process the files did not convert to mvf

can someone suggest me how to approach using this software

PS if it sounds stupid to anyone i apologize i am new at it,

Regards,

KiTri

[Jonathan]

Perhaps the best approach would be to rerun the alignment with a current MAQ version, and then try maqview with the new cns and new map again;

Otherwise I'd say it's like finding a needle in the haystack to pinpoint your problem!

Best
-Jonathan

[KiTrinet]

Hi Jonathan

thanks for the information. i tried to follow your direction but unfortunately the cns file is a binary file and i am failing towards converting to acgt.
my maq is the newest version so is the maqview.
After i try to run the data, i obtain this

<3125> 6/9/2009 1:01:06 PM
Element No.4 is not a number! P = t????2???{???mr???.??y^?WyM????)?u?k?N*zi%?QcJ?+f?Z?r?A?????FP?????V?}?4??A46???w??iA????6??]E????f5?@%???|??'g???q?D???V?b????u????q??ik??'G?dP?E???0P3a
<3728> 6/9/2009 1:01:08 PM
Element No.4 is not a number! P = ?U~3?X9?n=???26?A@??$??
<4244> 6/9/2009 1:01:09 PM
Element No.4 is not a number! P = ?
Line: ?)
<4733> 6/9/2009 1:01:11 PM
Element No.4 is not a number! P = ????l?U?1L9?%&??A
Line: ?????.?????:???????n?????x???3FEzPl?#\??|????t???}???????????}\C?,o|~8??t????`?$?J?(O?????H?E?p<?????P?}>?4?0?>=D ?p(
<5132> 6/9/2009 1:05:47 PM
MVFmaker Output: C:\Users\Ahmeti Inc\Desktop\30EFN.6\30EFN_6_30EFN_6.MVF
Total:269,760,457 (A:9,918,429 T:11,513,113 G:13,220,293 C:10,534,443 N:224,574,179)
READS SUM:0 [+]0 [-]0 [contains 'N']0
Mismatch:0 (0) (N:0)
Paired speed: --- MB/s Sort speed: 0.01 MB/s Conversion speed: 5.05 MB/s


can you please let me know what should i do in order to resolve this issue?
If possible please let me know I would be more than happy to share more information, I just dont know how other approach to do.
the entire process fails as i try to create the MVF file. when i go to MVFmaker the process starts it counts how many ATGCN i have but is not able to provide the final sequence.

thanks,

KiTri