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Included support for indel error detection and read filtering in CollectSamErrorMetrics #1370

Merged
merged 4 commits into from
Sep 24, 2019
Merged

Included support for indel error detection and read filtering in CollectSamErrorMetrics #1370

merged 4 commits into from
Sep 24, 2019

Commits on Sep 24, 2019

  1. Included support for indel error detection in CollectSamErrorMetrics 

    - Created new IndelErrorCalculator and IndelErrorMetric classes
- Adjusted CollectSamErrorMetrics to be able to consider insertions and
deletions, as well as number of inserted and deleted bases
- Tests for indel error detection
- Added indel_length stratifier
- The PairOrientation stratifier now checks if the read is paired and
returns null if it is not
- Using operator information to that has been incorporated into htsjdk
    @jonn-smith @michaelgatzen
    jonn-smith authored and michaelgatzen committed Sep 24, 2019
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  2. Impelemented minor PR comments

    @michaelgatzen
    michaelgatzen committed Sep 24, 2019
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  3. Manually merged iteration improvements 

    - Merged mg_longread_error_reporting_iteration into mg_longread_error_reporting
    @michaelgatzen
    michaelgatzen committed Sep 24, 2019
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  4. Minimal cosmetic changes

    @michaelgatzen
    michaelgatzen committed Sep 24, 2019
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