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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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genemetrics result different between 0.9.8 and 0.9.9 #773

Open pmtmarine opened 1 year ago

pmtmarine commented 1 year ago

cnary.py 

def by_gene(self, ignore=params.IGNORE_GENE_NAMES):
   ignore += params.ANTITARGET_ALIASES
   start_idx = end_idx = None (only del in 0.9.9 ? Why?)

something wrong in genemetrics result 

$ python3 cnvkit.py genemetrics sample.cnr >sample.final_gene.cnr

$ grep -w MYC sample.final_gene.cnr
chr8    128747718   128908053   MYC 6.36412 165 12089.4 9   8.6922

$ grep -w MYC sample.cnr -C 2
chr8    128429691   128588454   Antitarget  160.124 6.90919 0.970921
chr8    128588454   128747218   Antitarget  239.995 7.32225 0.986018
chr8    128747718   128748063   MYC 10755.5 6.03366 0.953326
chr8    128748291   128748580   MYC 13712.4 6.51247 0.956057
chr8    128748580   128748869   MYC 15145.9 6.23034 0.96773
chr8    128750493   128750750   MYC 14552   6.44618 0.965993
chr8    128750750   128751007   MYC 16226.7 6.50782 0.967813
chr8    128751007   128751265   MYC 14297.6 6.42488 0.966846
chr8    128752641   128752922   MYC 12428.5 5.86496 0.971669
chr8    128752922   128753204   MYC 11518.5 6.05504 0.969818
chr8    128753704   128908053   Antitarget  237.28  7.19697 0.972948
chr8    128908053   129062402   Antitarget  293.876 7.4257  0.981591

The end num should be 128753204 not 128908053 !!!!!!

pmtmarine commented 1 year ago

I found that the reasons for this difference were loc and iloc in cnary.py def by_gene