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Opticluster #297

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merged 76 commits into from Jan 5, 2017

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@mothur-westcott @pschloss
@mothur-westcott
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mothur-westcott commented Jan 5, 2017

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mothur-westcott and others added some commits May 2, 2016

@mothur-westcott mothur-westcott Begins opticluster efefe3e
@mothur-westcott mothur-westcott Datastructure for opticluster 6017479
@mothur-westcott mothur-westcott Setup function layout for opticluster 5249384
@mothur-westcott mothur-westcott WIP opticluster e8364d5
@mothur-westcott mothur-westcott WIP OptiCluster 1cd31f9
@mothur-westcott mothur-westcott Fixes extra outputdir in make.group e388662
@mothur-westcott mothur-westcott Adds opticluster to cluster command 6aeb716
@mothur-westcott mothur-westcott Adds opticluster to cluster.split command 1df3de2
@mothur-westcott mothur-westcott Fixed indexing issue in read 3bc3e8a
@mothur-westcott mothur-westcott Adds delta to cluster.split bfc064e
@mothur-westcott mothur-westcott Fixes bug with float values in biom file 41b77b2
@mothur-westcott mothur-westcott WIP OptiCluster fdb9865
@mothur-westcott mothur-westcott Adds dist parameter to cluster.split 
Outputs merged column matrix
 24bcf3e
@mothur-westcott mothur-westcott Adds count file to sens.spec 15ddbd2
@mothur-westcott mothur-westcott Fixes typo in error message 994b705
@mothur-westcott mothur-westcott Adds output files to opti method a33808f
@mothur-westcott mothur-westcott Opti cluster updates 348d347
@mothur-westcott mothur-westcott Optimizing opticluster 6b82388
@mothur-westcott mothur-westcott Trying to get Test project to link ebf672a
@mothur-westcott mothur-westcott Opticluster modifications 94ef310
@mothur-westcott mothur-westcott Test datasets for optimatrix d80a71a
@mothur-westcott mothur-westcott Working on testing for optimatrix 874ed0a
@mothur-westcott mothur-westcott Delete temp files in cluster.split 9badb05
@mothur-westcott mothur-westcott Adds column and count files for testing 9cc2265
@mothur-westcott mothur-westcott Adds new calcs to opticluster df7b5e7
@mothur-westcott mothur-westcott Bug fix make.contigs file divide 26a9a37
@mothur-westcott mothur-westcott Adds tests for optimatrix cbaf221
@mothur-westcott mothur-westcott Adds test for phylip file read 
Optimatrix
 547bdf7
@mothur-westcott mothur-westcott Adds unit tests for opticluster 90a0be5
@mothur-westcott mothur-westcott Removes testing duplicate symbols 74dbf25
@mothur-westcott mothur-westcott Adds singletons to stats for opticluster 3ffbf31
@mothur-westcott mothur-westcott WIP opticluster ca2b453
@mothur-westcott mothur-westcott Adds calcs and resolves extra names bug fcada69
@mothur-westcott mothur-westcott Adds sens.spec results to cluster.split fd79286
@mothur-westcott mothur-westcott Adds output to opticluster
25187e7
@mothur-westcott mothur-westcott WIP oneotu opticluster c310501
@mothur-westcott mothur-westcott Singleton randomization ebe6977
@mothur-westcott mothur-westcott Removes oneotu randomization 
Produced bad results
e64bd59
@mothur-westcott mothur-westcott Merge branch 'v.1.38.0' into Opticluster a591ad7
@mothur-westcott mothur-westcott Merges 1.38.0 into opticluster branch
6c5ebe5
@mothur-westcott mothur-westcott Changes project settings c49c0b5
@mothur-westcott mothur-westcott Sets threads for vsearch clustering
71f272f
@pschloss pschloss Merge in v.1.38.1 56f522b
@pschloss pschloss Merge in v.1.39.0 8d9afcb
@pschloss pschloss Remove extra threads line
41d92f2
@mothur-westcott mothur-westcott Changes group name error to warning 
Adjusts filenames
 9959ced
@mothur-westcott mothur-westcott Fixes hard issue in cluster commands
d018aab
@mothur-westcott mothur-westcott Hard cutoff change in sensspec
c7ce20c
@mothur-westcott mothur-westcott Fixes blank cutoff in sens.spec
ff065a5
@mothur-westcott mothur-westcott Removed unused files
d8d5d75
@mothur-westcott mothur-westcott Fixed negative values in opticluster for cluster command
4199174
@mothur-westcott mothur-westcott Fixes negative values and delta issue opticluster
ef324c8
@pschloss pschloss Make default value fo delta 0.0000
aae4a30
@mothur-westcott mothur-westcott Changed delta default in cluster.split
047cb3a
@pschloss pschloss Reduce default maxIters to 100
1084a73
@mothur-westcott mothur-westcott Fixes negative tn values in opti 
Caused by double instead of unsigned long long
10a6f19
@mothur-westcott mothur-westcott Fixes problem with insert location in opti
031e1b8
@mothur-westcott mothur-westcott Adds initialize parameter to cluster and cluster.split 
Opticluster
30d65f3
@mothur-westcott mothur-westcott Fixes help documentation
59b7d0a
@mothur-westcott mothur-westcott Fixes bug with running of sens.spec
d0d35b0
@mothur-westcott mothur-westcott Fixes overflow from numSeqs datatype
bdac507
@mothur-westcott mothur-westcott Fixes bug where matrix format could be confused if sequence names wer… 
…e all numeric

OptiCluster
4ec2078
@mothur-westcott mothur-westcott Adds timing to steps output
16fedfc
@mothur-westcott mothur-westcott Adds numOTUs to opti output
bab404d
@mothur-westcott mothur-westcott Adds numOtus to opti output
303a2d7
@mothur-westcott mothur-westcott Updates defaults for opti
50b3f8b
@mothur-westcott mothur-westcott WIP 338743f
@mothur-westcott mothur-westcott Removed redundant randomization. Took self bin count out of loop 
Optimization for time

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15302d5
@mothur-westcott mothur-westcott Merge pull request #286 from mothur/opti_improv_1 
Opti improv 1
fd2e6ba
@mothur-westcott mothur-westcott Working in progress with reducing memory for opti 20a419b
@mothur-westcott mothur-westcott Failed attempt to make phylip read faster a36a235
@mothur-westcott mothur-westcott Backing out of bad change 1d47492
@mothur-westcott mothur-westcott Changes to phylip read for memory reduction 
Optimatrix

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0b464e6
@mothur-westcott mothur-westcott Changes int to long long
61e5529
@mothur-westcott mothur-westcott Fixed issue with nameMap in optimatrix read
9ca9b2a
@mothur-westcott mothur-westcott Merge branch '1.39.0' into Opticluster

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25c446c

@mothur-westcott mothur-westcott merged commit df42fe0 into 1.39.0 Jan 5, 2017
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@mothur-westcott mothur-westcott deleted the Opticluster branch Jan 5, 2017

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