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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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v1.3 #121

Closed jluebeck closed 1 year ago

jluebeck commented 2 years ago

Version 1.3_r1 supports both python3 and python2. This release also corrects a bug in the visualization of amplicon copy numbers for genome segments < 50kbp and includes small improvements to seed filtering and merging of nearby segments. Complete changelog available here.

virajbdeshpande commented 2 years ago

May resolve merge conflicts and merge

jluebeck commented 2 years ago

Thanks, Viraj - let me know if there is anything I can do to help with resolving the merge conflicts. I think I don't have permissions to do it directly.

virajbdeshpande commented 2 years ago

Thanks, Viraj - let me know if there is anything I can do to help with resolving the merge conflicts. I think I don't have permissions to do it directly.

You need to merge vdeshpande:master into jluebeck:master. This will show you all the merge conflicts on your branch. You can then resolve those and stage and commit the files for which you fixed the merge conflicts. Once you push the new commit, Github should allow us to merge the branch into master.

jluebeck commented 1 year ago

Fixed all conflicts and merged into my fork. Should be ready to go!

jluebeck commented 1 year ago

Hi Viraj, it looks like only those with write access to the repository can merge the approved pull requests. Thanks!

Jens

virajbdeshpande commented 1 year ago

Thanks for the updates. Is this ready to merge?