1.39.0 #299

mothur-westcott · Jan 19, 2017

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mothur-westcott merged commit cfb593d into master Jan 19, 2017
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mothur-westcott deleted the 1.39.0 branch Jan 24, 2017

mothur-westcott	`Begins opticluster`		`efefe3e`
mothur-westcott	`Datastructure for opticluster`		`6017479`
mothur-westcott	`Setup function layout for opticluster`		`5249384`
mothur-westcott	`WIP opticluster`		`e8364d5`
mothur-westcott	`WIP OptiCluster`		`1cd31f9`
mothur-westcott	`Fixes extra outputdir in make.group`		`e388662`
mothur-westcott	`Adds opticluster to cluster command`		`6aeb716`
mothur-westcott	`Adds opticluster to cluster.split command`		`1df3de2`
mothur-westcott	`Fixed indexing issue in read`		`3bc3e8a`
mothur-westcott	`Adds delta to cluster.split`		`bfc064e`
mothur-westcott	`Fixes bug with float values in biom file`		`41b77b2`
mothur-westcott	`WIP OptiCluster`		`fdb9865`
mothur-westcott	`Adds dist parameter to cluster.split` Outputs merged column matrix		`24bcf3e`
mothur-westcott	`Adds count file to sens.spec`		`15ddbd2`
mothur-westcott	`Fixes typo in error message`		`994b705`
mothur-westcott	`Adds output files to opti method`		`a33808f`
mothur-westcott	`Opti cluster updates`		`348d347`
mothur-westcott	`Optimizing opticluster`		`6b82388`
mothur-westcott	`Trying to get Test project to link`		`ebf672a`
mothur-westcott	`Opticluster modifications`		`94ef310`
mothur-westcott	`Test datasets for optimatrix`		`d80a71a`
mothur-westcott	`Working on testing for optimatrix`		`874ed0a`
mothur-westcott	`Delete temp files in cluster.split`		`9badb05`
mothur-westcott	`Adds column and count files for testing`		`9cc2265`
mothur-westcott	`Adds new calcs to opticluster`		`df7b5e7`
mothur-westcott	`Bug fix make.contigs file divide`		`26a9a37`
mothur-westcott	`Adds tests for optimatrix`		`cbaf221`
mothur-westcott	`Adds test for phylip file read` Optimatrix		`547bdf7`
mothur-westcott	`Adds unit tests for opticluster`		`90a0be5`
mothur-westcott	`Removes testing duplicate symbols`		`74dbf25`
mothur-westcott	`Adds singletons to stats for opticluster`		`3ffbf31`
mothur-westcott	`WIP opticluster`		`ca2b453`
mothur-westcott	`Adds calcs and resolves extra names bug`		`fcada69`
mothur-westcott	`Adds sens.spec results to cluster.split`		`fd79286`
mothur-westcott	`Adds output to opticluster`		`25187e7`
mothur-westcott	`WIP oneotu opticluster`		`c310501`
mothur-westcott	`Singleton randomization`		`ebe6977`
mothur-westcott	`Removes oneotu randomization` Produced bad results		`e64bd59`
mothur-westcott	`Merge branch 'v.1.38.0' into Opticluster`		`a591ad7`
mothur-westcott	`Merges 1.38.0 into opticluster branch`		`6c5ebe5`
mothur-westcott	`Changes project settings`		`c49c0b5`
mothur-westcott	`Sets threads for vsearch clustering`		`71f272f`
pschloss	`Merge in v.1.38.1`		`56f522b`
pschloss	`Merge in v.1.39.0`		`8d9afcb`
pschloss	`Remove extra threads line`		`41d92f2`
mothur-westcott	`Changes group name error to warning` Adjusts filenames		`9959ced`
mothur-westcott	`Fixes hard issue in cluster commands`		`d018aab`
mothur-westcott	`Hard cutoff change in sensspec`		`c7ce20c`
mothur-westcott	`Fixes blank cutoff in sens.spec`		`ff065a5`
mothur-westcott	`Adds hard change to mgcluster and sens.spec`		`e1d80d9`
mothur-westcott	`Remove hard from mgcluster`		`53d2600`
mothur-westcott	`Removed unused files`		`d8d5d75`
mothur-westcott	`In script or batchmode - bail out of mothur` #212		`6f2cf2e`
mothur-westcott	`Fixed negative values in opticluster for cluster command`		`4199174`
mothur-westcott	`Fixes negative values and delta issue opticluster`		`ef324c8`
pschloss	`Make default value fo delta 0.0000`		`aae4a30`
mothur-westcott	`Changed delta default in cluster.split`		`047cb3a`
mothur-westcott	`Adds blastdir parameter to set.dir` #223		`3c6e19e`
mothur-westcott	`Updates related files to include blastLocation` #223	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`2ee0071`
mothur-westcott	`Merge pull request #266 from mothur/Blast_223` Blast 223		`bfc09fe`
mothur-westcott	`Adds taxonomy spaces to summary.tax`		`5a9d908`
pschloss	`Reduce default maxIters to 100`		`1084a73`
mothur-westcott	`Adds common functions to tax equalizer` #265		`72ec06e`
mothur-westcott	`Adds common functions to phylotype` #265		`c7179b4`
mothur-westcott	`Adds tax spaced read to sort.seqs` #265		`9ead811`
mothur-westcott	`Adds tax spaces to screen.seqs` #265		`b30ae5e`
mothur-westcott	`Adds tax space to pcr.seqs` #265		`14b21d3`
mothur-westcott	`Adds tax space to sub.sample` #265		`3caf426`
mothur-westcott	`Adds tax space to list/get/remove.seqs` #265		`0755b85`
mothur-westcott	`Adds tax space to get/remove.groups` #265		`1dba3f4`
mothur-westcott	`Adds tax spaces to get/remove.lineage` #265		`fadc872`
mothur-westcott	`Adds tax spaces to classify.otu` #265		`8d8485f`
mothur-westcott	`Adds tax spaces to common cons tax read` #265		`189fc44`
mothur-westcott	`Adds tax spaces to merge.taxsummary` #265		`8fe1e55`
mothur-westcott	`Fixes negative tn values in opti` Caused by double instead of unsigned long long		`10a6f19`
mothur-westcott	`Adds tax spaces to make.biom` #265		`395673a`
mothur-westcott	`WIP adding tests` #265		`5e7ff32`
mothur-westcott	`Fixes problem with insert location in opti`		`031e1b8`
mothur-westcott	`Adds initialize parameter to cluster and cluster.split` Opticluster		`30d65f3`
mothur-westcott	`Fixes help documentation`		`59b7d0a`
mothur-westcott	`Adds offByOne type to make.contigs`		`f82ae5a`
mothur-westcott	`Fixes bug with running of sens.spec`		`d0d35b0`
mothur-westcott	`Adds testing units for phylotree` #265		`19caf05`
mothur-westcott	`Fixes overflow from numSeqs datatype`		`bdac507`
mothur-westcott	`Fixes perfectMatch type make.contigs`	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`822ba85`
mothur-westcott	`Merge pull request #271 from mothur/TaxSpaces_265` Tax spaces 265		`a23ea7d`
mothur-westcott	`Fixes groupNames for 3 column format` Make.contigs #270	All checks have failed 2 errored checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build could not complete due to an error Details	`2838f9a`
mothur-westcott	`Merge pull request #272 from mothur/Make_File_270` Fixes groupNames for 3 column format		`32aafff`
mothur-westcott	`Fixes taxon_unclassified bug`		`ee7be1e`
mothur-westcott	`Adds tax spaces fix to consTax` #265		`a52462d`
mothur-westcott	`Makes repfasta and repname parameters optional` #32	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`2ff2527`
mothur-westcott	`Merge pull request #273 from mothur/Rep_32` Rep 32		`3f9606a`
mothur-westcott	`Changes optimization`		`b029499`
mothur-westcott	`Removes alphasort in precluster` #220		`2cd73cb`
mothur-westcott	`Uses mothurOut readNames` #220		`c2295de`
mothur-westcott	`Adds filter to aligned method pre.cluster` #220		`78d4a1c`
mothur-westcott	`Adds filter to improve time in pre.cluster` #220		`b33b1a4`
mothur-westcott	`Removes unused functions in sequenceDB`		`fef5caf`
mothur-westcott	`Adds gobble to groupFile read - get.seqs`		`6a9bc2a`
mothur-westcott	`Improves speed in pre.cluster` #220		`21e7117`
mothur-westcott	`Fixes windows compile issues`	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`d8b2ea8`
mothur-westcott	`Merge branch 'precluster_220c' into 1.39.0`		`278f690`
mothur-westcott	`Merge pull request #275 from mothur/precluster_220c` Precluster 220c		`56f379f`
mothur-westcott	`Improvements to memory pre.cluster`		`13647f8`
mothur-westcott	`Merge branch '1.39.0' of https://github.com/mothur/mothur into 1.39.0`		`7bc9807`
mothur-westcott	`Limits maxIters to numOtus sparcc`		`8497ed3`
mothur-westcott	`Fixes bug where matrix format could be confused if sequence names wer…` …e all numeric OptiCluster		`4ec2078`
mothur-westcott	`Fixes cutoff issue dist.seqs` #274		`924c670`
mothur-westcott	`Adds timing to steps output`		`16fedfc`
mothur-westcott	`Adds numOTUs to opti output`		`bab404d`
mothur-westcott	`Adds numOtus to opti output`		`303a2d7`
mothur-westcott	`Adds group selection to countParser` #220		`989ed99`
mothur-westcott	`Adds selectedGroups to sequenceParser class` #220		`ef289e2`
mothur-westcott	`Adds subsetGroups to Windows pre cluster` #220	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`0a2af8a`
mothur-westcott	`Merge pull request #279 from mothur/precluster_mem` Precluster mem		`86b5ed3`
mothur-westcott	`Updates defaults for opti`		`50b3f8b`
mothur-westcott	`Fixes groupIndex for selectedGroups option` Pre.cluster #220		`4d8056d`
mothur-westcott	`WIP`		`338743f`
mothur-westcott	`Removed redundant randomization. Took self bin count out of loop` Optimization for time	Some checks were not successful 1 errored and 1 successful checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`15302d5`
mothur-westcott	`Merge pull request #286 from mothur/opti_improv_1` Opti improv 1		`fd2e6ba`
mothur-westcott	`Working in progress with reducing memory for opti`		`20a419b`
mothur-westcott	`Failed attempt to make phylip read faster`		`a36a235`
mothur-westcott	`Backing out of bad change`		`1d47492`
mothur-westcott	`Changes to phylip read for memory reduction` Optimatrix	All checks have failed 2 errored checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build could not complete due to an error Details	`0b464e6`
mothur-westcott	`Starting vsearch capability for Windows` Vsearch disclaimer: This is a pre-release of VSEARCH 2.3.1 for 64-bit Windows. The binary is compiled with the mingw-w64 cross compiler. Not tested well. Not for production. Feel free to try it out!		`7ee85e3`
mothur-westcott	`Fixing bugs for Windows compile`		`933adb1`
mothur-westcott	`Changes int to long long`		`61e5529`
mothur-westcott	`Fixed issue with nameMap in optimatrix read`		`9ca9b2a`
mothur-westcott	`Adds vsearch for Windows to cluster`		`c893d7b`
mothur-westcott	`Adds vsearch for Windows to cluster.split`		`b580d0d`
mothur-westcott	`wip vsearch`		`bbc1603`
mothur-westcott	`Adds trim parameter to make.sra`		`8124aec`
mothur-westcott	`Converts seq to uppers if no trimming so barcodes can be removed` sffinfo		`6cbe048`
mothur-westcott	`Merge remote-tracking branch 'origin/1.39.0' into 1.39.0`		`06c3d20`
mothur-westcott	`Fixes bug with uchime location windows`		`18d0b2a`
mothur-westcott	`Merge branch '1.39.0' into Opticluster`	All checks have failed 2 errored checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build could not complete due to an error Details	`25c446c`
mothur-westcott	`Merge pull request #297 from mothur/Opticluster` Opticluster		`df42fe0`
mothur-westcott	`Fixes typos`		`57f2df0`
mothur-westcott	`Working on vsearch windows parallelization`		`b358d11`
mothur-westcott	`Default clustering method=opti`		`eba2e8b`
mothur-westcott	`Fixes bug with align report optimization` #288		`719e77e`
mothur-westcott	`Adds numSeqs to return values in sequenceParser classes`		`d10ca55`
mothur-westcott	`Removes windows paralellization code, uses vsearch parallelization` #215		`2ff08c3`
mothur-westcott	`Adds sequence parser return values to calling classes`		`bf8bc84`
mothur-westcott	`Merge branch '1.39.0' into Windows_vsearch`	All checks have failed 2 errored checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build could not complete due to an error Details	`3d3d27f`
mothur-westcott	`Merge pull request #298 from mothur/Windows_vsearch` Windows vsearch		`f3cad7b`
mothur-westcott	`Merge branch 'master' into 1.39.0`		`2db8466`

mothur/mothur

1.39.0 #299

mothur-westcott commented Jan 19, 2017

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

mothur-westcott merged commit `cfb593d` into master Jan 19, 2017
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mothur-westcott deleted the 1.39.0 branch Jan 24, 2017

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mothur-westcott commented Jan 19, 2017

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

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Hide details View details mothur-westcott merged commit cfb593d into master Jan 19, 2017 1 check was pending

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mothur-westcott deleted the 1.39.0 branch Jan 24, 2017

mothur-westcott merged commit `cfb593d` into master Jan 19, 2017
1 check was pending