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Grade adapter, overrepresented, N content and duplication as FastQC - #146
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Four modules were graded against cutoffs in different units from the values compared with them, or on a different quantity from the one the report shows: - overrepresented: the value was a fraction of reads, the default cutoffs (0.1, 1) are percent, so the effective cutoffs were 10% and 100%. The grade is now the percentage of the top sequence in the reported list (zero if the list is empty), as in FastQC, so a sequence below the list's own cutoffs can no longer raise it. - adapter: the value was the largest per-position count of an adapter start, while the report (and FastQC) shows the cumulative percentage of reads with the adapter at or before each position. The grade is now the maximum of that cumulative percentage. - n_content, duplication: fractions compared with fractional default cutoffs, which worked, but a config file in the FastQC limits.txt format (percent: n_content 5/20, duplication 70/50) made N content unable to warn and duplication always fail. Both are now graded in percent and the defaults are given in percent, like every other module and like Configuration/limits.txt. Also, for modules where higher is worse, a value equal to a cutoff no longer reaches it (FastQC tests value > cutoff), e.g. a sequence at exactly 0.1% passes. data/test_data/md5sum.txt: bam_2 now warns for overrepresented sequences (top sequence 0.12% of reads), as FastQC 0.13.0 does.
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Fixes #145.
Configuration/limits.txt. With the default cutoffs their grades do not change.value > cutoff); e.g. a sequence at exactly 0.1 % passes.data/test_data/md5sum.txt:bam_mult_out/bam_2now warns for overrepresented sequences (top sequence 0.12 % of reads), as FastQC 0.13.0 does. No other test output changes.Tested: all 17 tests pass (Linux, GCC 14, main @ 99197e7). On the file from #145 and on
bam_2.bamthe four grades this PR touches now match FastQC 0.13.0 (on the #145 file every module does), and all other sections offastqc_data.txtare unchanged.