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genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
GNU General Public License v3.0
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Optimized #1

Closed marghoob closed 10 years ago

marghoob commented 10 years ago

This will need some thorough testing before it can be merged to master--I see small differences in the close-end map counts in the logs, but the far-end checksums match. Also, make sure that the platform being used is an Intel machine with SSE 4.2 support and atleast 20 GB of RAM (since the index for whole-genome is around 15 GB).

liangkaiye commented 10 years ago

got an error message.

vpn-10-1-24-9:bina Ye$ git pull https://github.com/BinaTechnologies/pindel optimized fatal: Not a git repository (or any of the parent directories): .git

On 10/28/13 3:25 AM, Marghoob Mohiyuddin wrote:

git pull https://github.com/BinaTechnologies/pindel optimized

marghoob commented 10 years ago

This is because the directory where you are running the command from, is not a git repository. I think you don't want to merge right now, so try cloning instead "git clone -b optimized git@github.com:BinaTechnologies/pindel.git" to try out the branch first. Once you are satisfied, you can then run "git pull https://github.com/BinaTechnologies/pindel optimized" in the directory containing your local copy of the pindel repo to merge the pull request--you can also merge the pull request graphically by clicking some buttons on the pull request page.

liangkaiye commented 10 years ago

ok, let me first review your code. we have a grant due in one week. I have to write 10 pages this week. will try to merge ASAP.

thanks and sorry to let you wait.

On 10/28/13 11:43 AM, Marghoob Mohiyuddin wrote:

This is because the directory where you are running the command from, is not a git repository. I think you don't want to merge right now, so try cloning instead "git clone -b optimized git@github.com mailto:git@github.com:BinaTechnologies/pindel.git" to try out the branch first. Once you are satisfied, you can then run "git pull https://github.com/BinaTechnologies/pindel optimized" in the directory containing your local copy of the pindel repo to merge the pull request--you can also merge the pull request graphically by clicking some buttons on the pull request page.

— Reply to this email directly or view it on GitHub https://github.com/genome/pindel/pull/1#issuecomment-27229484.

marghoob commented 10 years ago

I am not in a hurry to merge--please make sure you are totally okay before merging. And feel free to ask any questions you may have. Good luck for your grant proposals.

nnutter commented 10 years ago

This pull request is being closed since it has been inactive for at least two weeks but can be reopened once either party has time to actively participate. Closing does not remove any prior conversation or content and only serves to keep the dashboard of open pull requests concise.