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karel-brinda / ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
https://arxiv.org/abs/1712.01146
MIT License
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Filtration by flags #22

Open karel-brinda opened 7 years ago

karel-brinda commented 7 years ago

Add support for following samtools mpileup options:

  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset []
  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set
                                            [UNMAP,SECONDARY,QCFAIL,DUP]