What is the status of coverageCount?

[John Blischak]

Hi,

I noticed that Subread 1.6.3 no longer builds the executable coverageCount. Was this intentional? There is no mention in the changelog that this feature was deprecated. Also, I couldn't find anything when I searched the mailing list for coverageCount.

Here are the steps I took to verify this:

docker run -it --rm ubuntu
apt-get update
apt-get install -y gcc make wget zlib1g-dev
# 1.6.2
wget https://downloads.sourceforge.net/project/subread/subread-1.6.2/subread-1.6.2-source.tar.gz
tar xzf subread-1.6.2-source.tar.gz
cd subread-1.6.2-source/src
make -f Makefile.Linux
cd ../..
#1.6.3
wget https://downloads.sourceforge.net/project/subread/subread-1.6.3/subread-1.6.3-source.tar.gz
tar xzf subread-1.6.3-source.tar.gz
cd subread-1.6.3-source/src
make -f Makefile.Linux
cd ../..
# Compare
diff <(ls subread-1.6.2-source/bin/) <(ls subread-1.6.3-source/bin/)
diff <(ls subread-1.6.2-source/bin/utilities/) <(ls subread-1.6.3-source/bin/utilities/)
# 1d0
# < coverageCount

Thanks,

John

[Wei Shi]

Unfortunately we have decided to discontinue this function. 

[John Blischak]

Hi Wei,

Thanks for the quick response. Would it be possible to update the changelog so that users know this function has been removed?

Thanks,

John

[Wei Shi]

Apologies for omitting this in the release note of version 1.6.3. I have just updated the release note.

Wei

[John Blischak]

Great. Thanks!