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Extend bamPEFragmentSize #577

@dpryan79

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@dpryan79

This was requested by @steffenheyne. In short, it'd be nice if bamPEFragmentSize could completely replace picard CollectInsertSizeMetrics. That produces the following:

  • MEDIAN_INSERT_SIZE
  • MEDIAN_ABSOLUTE_DEVIATION
  • MIN_INSERT_SIZE
  • MAX_INSERT_SIZE
  • MEAN_INSERT_SIZE
  • STANDARD_DEVIATION
  • READ_PAIRS
  • WIDTH_OF_10_PERCENT
  • WIDTH_OF_20_PERCENT
  • WIDTH_OF_30_PERCENT
  • WIDTH_OF_40_PERCENT
  • WIDTH_OF_50_PERCENT
  • WIDTH_OF_60_PERCENT
  • WIDTH_OF_70_PERCENT
  • WIDTH_OF_80_PERCENT
  • WIDTH_OF_90_PERCENT
  • WIDTH_OF_99_PERCENT

I'm going to skip PAIR_ORIENTATION, since basically everything will be FR these days. WIDTH_OF_50_PERCENT is of course the same as the median, no clue why both are present.

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