Merge from central.
Merged from central.
add SHRiMP mapper for short read tools
Updating security from central
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merging heads
merging heads
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merge heads
Fix a bug in shrimp_wrapper and add a tool to split paired-end reads.
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Commiting changeset to security
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Merging heads
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Updating security from central
Merging heads
Merging heads
Merging heads
Merged from central, resolved 2 conflicts in tools/actions/__init__.py
and tools/parameters/basic.py