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jipingw / DegNorm

An R package for Degradation Normalization for RNA-seq data
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Wrong variable? #6

Open knokknok opened 2 months ago

knokknok commented 2 months ago

https://github.com/jipingw/DegNorm/blob/2e3e9c950849869289b8651f8c735aba4774cff5/R/coverage_cal_functions.R#L33

Should be

       if(!file.exists(paste(bam_file_list[k],".bai",sep=""))){

?

jipingw commented 2 months ago

sample_names were simplified version of bam_file_list names after stripping out those characters for file path/extension etc. the code should be fine.

knokknok commented 2 months ago

sample_names were simplified version of bam_file_list names after stripping out those characters for file path/extension etc.

Yes, therefore the files paste(sample_names[k],".bai",sep="") will never exist and the bam files reindexed systematically.