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Ran 07 Jul 2015 10:40AM UTC

Files 3

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Committed 07 Jul 2015 10:26AM UTC coverage: 71.86% (-6.4%) from 78.228%

Job # 91.2

Build Type

push

travis-ci

Committed by

SamStudio8

Commit Message

Use 0-index for sequence data. is_seq now is_pos.

* `is_seq` argument to initialisation removed and replaced with `is_pos`.
* Use `is_pos` to indicate the expected input is positional, not sequence.
* Force use of `PositionCounterStrategy` when `is_pos` is True.
* Sequence data now read in to 0-indexed arrays to avoid the overhead of string
  re-allocation by having to append a padding character to the beginning of very
  long strings.
* Region metadata continues to use 1-indexed positions for user output.
* `VariantCounterStrategy` now `PositionCounterStrategy`.
* `PositionCounterStrategy` expects 1-indexed lists of positions;
  `prepare` populates the listed locations with 1 and then `evaluate`
  returns the sum as before.
* `test_regression2` updated to account for converting 1-index to 0-index when
  manually handling the sequence for expected results.

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309 of 430 relevant lines covered (71.86%)

0.72 hits per line

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