bigdatagenomics / adam / 4045 / 1

Ran 12 Dec 2018 06:58PM UTC

Files 142

Run time 18s

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Committed 12 Dec 2018 06:58PM UTC coverage: 79.121%. Remained the same

Job # 4045.1

Build Type

push

jenkins

Committed by Michael L Heuer

Commit Message

[ADAM-2102] Inverted duplicates are not found in mark duplicates (#2101)

* Inverted duplicates are not found in mark duplicates

Mark duplicates uses the left and right positions corrected for clipping
to match duplicates on coordinates. However, this approach can miss
duplicates that are truly inverted (ie positions reversed and the
strand direction is reversed).

Picard and sambamba pick up these reads as duplicates

This change fixes this issue by checking the direction when doing the
left and right group bys in mark duplicates.

* Revert incorrect formatting changes

* Revert incorrect formatting changes

Coverage Stats

6700 of 8468 relevant lines covered (79.12%)

0.79 hits per line

bigdatagenomics / adam / 4045 / 1

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