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gmarocena / gasv

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Nonreciprocal invalid? #4

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Hello,

I've just started trying to use GASV in the last week.  Today, I got the 
following error when I tried to add nonreciprocal:

Exception in thread "main" java.lang.IllegalArgumentException: Unrecognized 
option: --nonreciprocal
        at gasv.main.GASVMain.parseOptions(GASVMain.java:465)
        at gasv.main.GASVMain.main(GASVMain.java:521)

I had entered:
/usr/java/latest/bin/java -jar ~/software/gasv/lib/gasv.jar --cluster --lmin 
150 --lmax 411 --maximal --nonreciprocal --minClusterSize 10 --outputdir 
~/analysis/ --verbose ~/analysis/file_all.deletion.retained.sorted

I had downloaded version 1.5.1

Is this not the proper way to add reciprocal?

Thanks,
Rose

Original issue reported on code.google.com by branno...@gmail.com on 21 Feb 2012 at 10:29

GoogleCodeExporter commented 8 years ago 
Dear Rose,

Thank you for your interest in GASV. There is a typo in the GASV documentation, 
the correct command line argument to turn off reciprocal clustering is 
"--noreciprocal"

Please let us know if this helps an if you have any other questions about GASV. 
We will fix this issue in our next update.

Thanks,

Suzanne

Original comment by sora...@gmail.com on 21 Feb 2012 at 11:44

GoogleCodeExporter commented 8 years ago 
Hi Rose,

We have just posted a fix to GASV which fixes the typo in GASV documentation. 
Now the command line argument agrees with the documentation.

These fix was posted as part of a small update and is available in 
GASV_RELEASE_1.5.2.tgz.

Thanks,

Suzanne

Original comment by sora...@gmail.com on 12 Apr 2012 at 7:15

GoogleCodeExporter commented 8 years ago

Original comment by sora...@gmail.com on 30 Apr 2012 at 4:24