f42bb86bdd
Only try to clip adaptors when both reads of the pair are on opposite strands
-- Read pairs that have unusual alignments, such as two reads both oriented like:
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<-----
where previously having their adaptors clipped as though the standard calculation of the insert size was meaningful, which it is not for such oddly oriented pairs. This caused us to clip extra good bases from reads.
-- Update MD5s due change in adaptor clipping, which add some coverage in some places
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| .. | ||
| CNV | ||
| coverage | ||
| qc | ||
| readutils | ||
| variantutils | ||
| BAQIntegrationTest.java | ||