[ruanjue]

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

[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

[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.

[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]

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]

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.

[fadista]

I am having the same problem. Did you find a way to solve the problem?

[fadista]

Hi,

Did you get your problem solved? I am having the same problem...

[AnamikaDarwin]

maqview freeglut error

Did you index the map with maqindex -c XXXX.cns YYYY.map ?

Hello,

I am having similar issues like other users, i.e. get the following error message:

maqview s512.3diff.mapMerge
freeglut /maqview/bin/maqview: relocation error: /maqview/bin/maqview: symbol __fprintf_chk, version GLIBC_2.3.4 not defined in file libc.so.6 with link time reference

I have indexed my .map and .cns file as suggested by ECO.

The .map and .cns files are generated by the 0.7.1 version of maq and I am using the latest version of maqview, 0.2.5.

Thanks!
Anamika

[Torst]

I too am getting a segmentation fault. It happens with all combinations of maqview 0.23/0.25 with maq 0.6/0.7.1

maqindex -i neg.map
-- Indexing the alignment file 'neg.map' ... Segmentation fault

This is on Centos 5.x, Xeon SMP 64 bit CPU, 64 GB RAM.

[seqfast]

same for me, just downloaded and installed, and ran the maqdemo on phiX (~6kb)

new MAQ 7.1, new maqview 2.5

rhel5, 16Gb RAM

2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux

/MAQ_BWA/maqview/maqindex -i -c consensus.cns all.map
-- Indexing the alignment file 'all.map' ... Segmentation fault


Incidentally I segfault while trying to build indexes with SOAPalign for anything larger than ~15Mbases.

[sigusn]

Hi
I just downloaded the latest MAQ and MAQviewer, and when I try to view my alignments, MAQview shuts down after few mouse clicks and scrolling with the message: "Bus error". Is there a limitation for the number of alignments that MAQview can handle ?

[xuer]

again maqview

I am sorry, is it because I made some mistake? with maqview -0.2.5, I got a blank window showing nothing sequence
after i close the window, I got a error:
freeglut_structure.c:439: fgEnumWindows: Assertion `fgState.Initialised' failed.

any one else have such problem ?

[baohua100]

You can use MapView to view any format alignment results.

http://evolution.sysu.edu.cn/english/software/mapview.htm

Now can be downloaded from our lab website.

View short reads alignment

input file:
1. Reference sequence file and
2. Eland , SOAP, MAQ, SeqMap ... any formated alignment results file

MapView converts the input files to MSF format file.

MapView loads the MSF file，then you can view the alignment and SNPs.

[lh3]

Jue has just uploaded a new maqview-0.2.5. This version works with 0.7.x. Sorry for the late update.