Feature skip softclip #1293
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Feature skip softclip #1293
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- soft-clipped regions are ignored and not returned
- inserts and padding should not be affected - soft clipping should be similar to matches_only
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This pull request addresses issue #1292.
It introduces a new option to pysam.AlignedSegment.get_aligned_pairs:
skip_soft_clippingSoft clipping are discarded (similarly to what happens to them with the matches_only), but keeps all other features (matches, inserts, deletions, skip and padding).
I've expanded the test to cover the modified line 2052, making sure that soft-clippings are discarded, whereas inserts and padding remain unaffected by the new option.