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IUPAC symbols for orig-dups mode: non-ACGT (case insensitive) are converted to N - #147
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…cates analysis here
…alizing original duplication data structures to original_duplicates.cpp
…ps_bam and init_orig_dups_fq to convert all non-ACGT letters to N prior to forming a falco_word when initializing the unique 'reads' for original duplicates analysis
…e htslib headers will be visibile when making original_duplicates.o
…n complementing the already reversed read sequence for revcomp mappers
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.
…cates analysis here
…alizing original duplication data structures to original_duplicates.cpp
…ps_bam and init_orig_dups_fq to convert all non-ACGT letters to N prior to forming a falco_word when initializing the unique 'reads' for original duplicates analysis
…e htslib headers will be visibile when making original_duplicates.o
…n complementing the already reversed read sequence for revcomp mappers
…de/falco into fix-iupac-issue-for-orig-dups
…bols ensuring all are treated like N
…ring all non-ACGT are treated like N
… running in orig-dups mode
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