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jts / mbtools

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NA #6

Closed vinodsinghjnu closed 9 months ago

vinodsinghjnu commented 9 months ago

It seems bam2pat for nanopore data has some problem in recognising "eXtended CIGAR", or CIGARX string. 

8,229,233,213,224,53,229,57,235,252,255,255,115,249,247,185,231,247,57,139,181,235,251,74,126,165,34,254,255,170,186,193,255,255,254,241,235,237,255,255,254,238,225,14,254,238,253,255,66,254,254,247  RG:Z:c969ee83   mc:f:99.5874    mg:f:99.6108    NM:i:72     
[ patter ] [ patter ] Unknown CIGAR character: =                                                                                                                                                      
[ patter ] [ chr9 ] Exception while processing line 798. Line content:                                                                                                                                                                                              
m64101_220704_113609/114427486/ccs      0       chr9    239949  60      8034=1I565=4D2297=      *       0       10900   ATTTCCAGTTATTCACATTAGAAACAGTACACCACTGAATAAATTTATGCATTCATCTTTGCTTACCTCTTTAATGATTCTTCACGATAAATGCTAGAAATAGAACCACAGACTTAAAGGTCTCCATTGATATGTGTGGC
jts commented 9 months ago

bam2pat seems to be a function in wgbs_tools, not mbtools. Did you mean to open this issue in their repo?

vinodsinghjnu commented 9 months ago

bam2pat seems to be a function in wgbs_tools, not mbtools. Did you mean to open this issue in their repo?

Sorry, I mistakenly posted on your GitHub account.