[Genome] Question about hgGcPercent program

[Brooke Rhead]

Hello Xueya,

I spoke to the developer who added the bedRegionIn and bedRegionOut 
options to the hgGcPercent program.  He said that your syntax looks 
correct, except that 'noLoads' should be written as 'noLoad'.  If you 
change that and still see the problem, perhaps you could send us your 
input file, or a sample of your input file to help us debug the program. 
  (No need to cc the whole list for that . . . attachments get stripped 
by our mailing list software, anyway.)

Let us know if the first fix does not resolve the issue.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Xueya Zhou wrote:
> Dear UCSC Genome Browser Crews,
> 
> I encountered a problem when using your hgGcPercent program to calculate GC
> percentage in regions that I specified in a bed file (in.bed).
> 
> The command line I used looked like the following:
> 
> hgGcPercent -bedRegionIn=in.bed -bedRegionOut=out.bed -doGaps -noLoads hg18
> hg18.2bit
> 
> Then It seemed that the program ignored the bed file that I provided, and
> went on directly to calculate the whole genome GC percent with the default
> window size. It produced gcPercent.bed file that detailed the GC percent in
> each region across whole genome, and  produced the empty file out.bed which
> was really wanted.
> 
> I have checked that both the file format and my command spelling were
> correct. I also had a glance at the source code
> kent/src/hg/makeDb/hgGcPercent/hgGcPercent.c, it did process the options of
> bedRegionIn and bedRegionOut.  So I was puzzled about what is going wrong.
> Could you help me figure it out? Thanks!
> 
> Xueya
>