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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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bam2pat for nanopore data has some problem in recognising CIGARX string #52

Open vinodsinghjnu opened 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
nloyfer commented 6 months ago

Thank you for bringing this to my attention. I added support for CIGARX strings

vinodsinghjnu commented 6 months ago

Thankyou nloyfer for resolving the issue of the handy tool.