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ARUP-NGS / BMFtools

Barcoded Molecular Families
MIT License
22 stars 8 forks source link

Dev #18

Closed dnbaker closed 9 years ago

dnbaker commented 9 years ago
  1. Metal:
    1. bmftools dmp re-working Estimate: 2-3 days
      1. Finish the Fisher Flattening. The new merging style should happen before a new "release" is made
      2. GATK Compatibility - provide options for mean quality score or max quality score for merged quality rather than the Fisher work
    2. Change the PV/FA/DR/DG tags to use array buffers, now that pysam has been expanded to be able to work with binary array tags.[COMPLETED]
  2. Functionality:
    1. bmftools dmp subcommand
    2. bmftools fully-piped dmp fastq's to tagged/mpa'd bams subcommand. (Code written, with a small bug fix in the works for non-HG37 datasets.) [COMPLETED]
      1. Currently recommended: PipeAlignTag.
  3. Testing:
    1. Bam tagging unit tests

Tabled:

  1. Quality score rescaling
  2. SampleMetrics/ReviewDir
  3. Bam rescue merging