change multiple-hit scoring
change multiple-hit scoring

Use NH (Number of Hits) tag rather than IH (number of Included Hits in
file) tag for multiple-hit fractional scaling. However, always record
one alignment in the total alignment count, rather than fractional
counts. This might lead to discrepancy in coverage and total number of
reads used, but we’re already potentially scaling via other means
anyway, and this new method should be more representative of actuality.
Besides, not everyone includes more than one hit in alignment results,
so using IH is disingenuous and misleading to documentation.

tjparnell/biotoolbox