Problem with navigation within the alignment track

[Chris]

Dear Savant developers and community,

I have a problem with strange jumps in the navigation (scrolling, moving left/right) within an alignment track.

All I did was:
1. Downloaded recent Version 2.0.3 for Linux systems (tested 64-Bit and 32-Bit on two different Unix environments; debian and ubuntu)
2. Started Savant with the .sh-script and selected the human genome hg19 (only sequence, no gene track or else)
3. Loaded my favorite alignment in bam-format (.bai index file in the same directory)
4. Jumped to some random location (let's say chr1:1000000-1000100) and looked at the reads

So far, so good. But when I drag the alignment track with the mouse or use the buttons on the top right, the alignment jumps to some other location at the 5' end of the genome (for example chr1: 1 - 999) and tells me "No data in range". Well, this is true, there is no alignment, but the region is not what I expected.

Is this a (known) bug? Or did I miss anything in the configuration or preferences of Savant?
Would be really for any help or ideas, since Savant looks like a very nice tool and I'd love to try it on my data.

Kind regards,
Christoph

[Anne-Sophie Sertier]

Dear Savant developers and community,

I'm dealing with the same issue, on Mac OS lion. When I try to zoom in or out, the location always returns to chr1: 1 - 1. This tool looks like very good to analyse structural variants (which is my goal).
Thanks a lot for reply,

Best regards,
Anne-Sophie

[Marc Fiume]

Hi All,

This may be related to your computer's localization, and an improper parsing of numbers on our part. Is your localization set to some language other than English? If so, please provide details.

Marc

[Chris]

Hi Marc,

these are the locale setting of my Unix distribution:

LANG=en_US.UTF-8
LANGUAGE=
LC_CTYPE=de_DE.UTF-8
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE=de_DE.UTF-8
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES=de_DE.UTF-8
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=

It is (mostly) set to the English (US) language (esp. "LANG=en_US.UTF-8"). I'm not really confident with all the minor details (the missing "LANGUAGE" and "LC_ALL" settings or the german setting "LC_CTYPE=de_DE.UTF-8" or "LC_CTYPE=de_DE.UTF-8"). Could this be a problem?

Thanks for your help here!
Best,
Christoph

On Tuesday, May 21, 2013 7:06:41 PM UTC+2, Chris wrote:

[Chris]

Hi again,

problem solved! I now changed all the remaining locale variables to "en_US.UTF-8" with

export LANGUAGE=en_US.UTF-8

.... and so on ...

and Savant now zooms, pans jumps correctly across the genome.
Thanks a lot for the tip!

Kind regards,
Christoph

[Maxime HEBRARD]

Hi,

I reply to this topic becouse I have the same problem.

My ubuntu is configure in french ($LANG=fr_FR.UTF-8).

we don't have the same separator for numbers so there is probably a parsing problem
cause that browser go to chr#:1-1 when I want to go chr#:1000-1500 for example
(like Chris problem, bug with zoom, or scrolling)

If I switch my Ubuntu in english ($LANG=en_US.UTF-8)
everything work well

Question : Can I keep my computer in french and specify to Savant browser to run in english ?

Regards
Maxime HEBRARD