[Genome] Liftover dies when using BED files with 12 fields?

[John Major]

Hello Hiram-

I am using the binary, for the PPC MAC.

John

Hiram Clawson wrote:

> Good Morning John:
>
> Are you using the WEB site for this liftOver operation, or are
> you using the liftOver binary in a local situation there ?
>
> We're missing some functionality in some of our utilities that do
> not properly recognize this column nine in its new form of r,g,b
> numbers.  It used to only be a 0 at all times.  I have recently fixed
> one of these situations, I would like to fix this one you mention.
>
> As a work-around, although you lose your r,g,b specification, turn
> that column 9 into a 0 and then it will lift.
>
> --Hiram
>
> John Major wrote:
>
>> Hello UCSC folks-
>>
>> I am trying to convert a large # of BED files from DM2 to DM3.
>> These files are all BED files using all of the 12 allowed fields ( 
>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED ).
>>
>> And example line from my BED file is:
>> (space separated)
>> chr4 646375 646462 miR-1000 0 + 646375 646462 255,0,0 2 42,41 0,46
>> chrX 12896008 12896104 miR-1026 0 + 12896008 12896104 255,0,0 2 47,44 
>> 0,52
>>
>> When I try to run liftover on these files, I get the following error:
>>
>> --Reading liftover chains
>> --Mapping coordinates
>> --invalid unsigned number: "255,0,0"
>>
>> According to the documentation for liftover, I should be able to use 
>> valid BED files.  These BED files are displayed properly via the 
>> Genome Browser, so am i missing something obvious here?  Do I need to 
>> enclose the last 4 fields in some kind of quotes?  Or does liftover 
>> not actually work with the last 4 BED file fields?
>>
>> thanks!
>> john major
>
>