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Type: Bug
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 1.15
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Component/s: Basic-Nucl, Basic-Protein, Workflow
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Tests Type:Untestable
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Sprint:DEV-16/10/2014, DEV-06/11/2014, DEV-13/11/2014
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Affect Type:Userdefined
Remote BLAST has the option HITLIST_SIZE: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node37.html
It is the limit of results count. And this option is called "Max hits" in UGENE.
HITLIST_SIZE is only the remote BLAST option:
Irrelevant to wwwblast and standalone commandline BLAST.
UGENE tries to emulate this option for local BLAST with other ones.
BLASTALL:
-K Number of best hits from a region to keep. Off by default.
If used a value of 100 is recommended. Very high values of -v or -b is also suggested [Integer]
BLAST+:
-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
But it is still called "Max hits". I think that it is wrong because 3 different options are called equally.
Consider two solutions and choose one of them:
1) Rename the options for BLASTALL and BLAST+.
2) Leave this name "Max hits" for the option but implement it with another way: take only first "Max hits" results and throw away other results. This solution could be wrong, investigate it.
Don't forget to synchronize the changes with the corresponding Workflow Designer elements.
- relates to
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UGENE-3083 Add "Max hits" parameter to local BLAST workflow elements
- Closed