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

[Hiram Clawson]

John:

Please try out these updated liftOver binaries:
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/liftOver.v151.MacOSX.ppc
ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/liftOverMerge.v151.MacOSX.ppc

They will lift these bed files with the r,g,b string in column 9.  I see they have
an annoying side effect of turning the r,g,b string into an integer, but that integer
will still result in the desired color.  I now need to fix that output so the r,g,b
string will remain as-is and not turn into an integer.

--Hiram

John Major wrote:
> 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
>>
>>
>