[Genome] Question about hgGcPercent program

[Xueya Zhou]

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

-- 
Xueya Zhou

Bioinformatics Division, Tsinghua National Laboratory of Information Science
and Technology

Address:    FIT 1-107, Tsinghua University, Beijing 100084, China

Phone:       +86-10-6279-5578 ext 822