mbias --keepDupes and -F argument parsing

[bwlang]

Maybe this is related to #58 ... but for mbias.

To get duplicates to be included I had to include both -F and --keepDupes:

MethylDackel mbias --noSVG --keepDupes -F 2816 -@ 1 -r plasmid_puc19c grch38_core+bs_controls.fa EM-seq-2hr-4ul-2.md.bam | head -n 2
Strand	Read	Position	nMethylated	nUnmethylated
OT	1	1	4211	14

I thought the --keepDupes was not necessary, but it seems to be:

MethylDackel mbias --noSVG  -F 2816 -@ 1 -r plasmid_puc19c grch38_core+bs_controls.fa EM-seq-2hr-4ul-2.md.bam | head -n 2
Strand	Read	Position	nMethylated	nUnmethylated
OT	1	1	20	1

however --keepDupes is not sufficient:

MethylDackel mbias --noSVG  --keepDupes -@ 1 -r plasmid_puc19c grch38_core+bs_controls.fa EM-seq-2hr-4ul-2.md.bam | head -n 2
Strand	Read	Position	nMethylated	nUnmethylated
OT	1	1	20	1

Perhaps related... octal notation seems strange too: I thought -F would override --keepDupe, but it does not seem to.

MethylDackel mbias --noSVG --keepDupes  -F 0xF00 -@ 1 -r plasmid_puc19c grch38_core+bs_controls.fa EM-seq-2hr-4ul-2.md.bam | head -n 2
Strand	Read	Position	nMethylated	nUnmethylated
OT	1	1	4211	14

note: I expect a lot of dups in this library.