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chloroExtractorTeam / chloroExtractor

MIT License
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Insert_size calculation bug #95

Open PfaffS opened 6 years ago

PfaffS commented 6 years ago

When in the scr-ref.bam no paired reads are mapped, the script scale-reads.pl will divide by 0. It tries to print the mean of all paired mapped reads template lengths (TLEN 9th column in .bam). If there are no paired reads it will try to calculate it by dividing by 0.

PfaffS commented 6 years ago

Fixed in https://github.com/chloroExtractorTeam/chloroExtractor/tree/fix_scr_tlen_spfaff

greatfireball commented 6 years ago

I would like to add a test for that bug to guarantee its fix inside the source code. Due to I only need to test scale-reads.pl i will need some reads which just map single end. Are your reads available? I do require about 10k read pairs.

greatfireball commented 6 years ago

Reopened because of missing test

greatfireball commented 6 years ago

Are you able to provide a testset @PfaffS ?

greatfireball commented 6 years ago

Just bumping up the issue again @PfaffS

How about writing a test?

greatfireball commented 6 years ago

And once more @PfaffS