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@mothur-westcott mothur-westcott released this Sep 30, 2019 · 5 commits to master since this release

  • Adds list to split.groups #624
  • Adds estimator.single command. #164
  • Passes CXX variables to uchime makefile. #614
  • Modifies output files from dist.shared, summary.single and summary.shared. You may run with or without rareification, but not both. #607
  • Improves speed and resource management for align.seqs command. #647
  • Improves mothur's logging features.
  • Adds qfile option to make.contigs. #650
  • Adds auto decompress feature to make.contigs if gz read fails. #634
  • Improves speed of dist.seqs and pairwise.seqs. #653
  • Adds 2 column pacbio file option to fastq.info. #649
  • Windows users can now run make.contigs with *.gz files.

Bugs:

  • Removes empty groups before printing count table. #641
  • Changes datatype for opti method to correct overflow.
  • Makes current file class thread safe. Caused random crashes in pre.cluster. #643
  • get.oturep command wasn't handling multiple labels. Removed labels parameter and modifies cutoff to act like cluster commands. ie. cutoff=0.01-0.03. #656
  • Trim.seqs was not removing paired primers. #667

Binaries:

  • Mac Version requires OSX 10.14 or higher
  • Windows 10 or higher
  • RHEL 7 or greater / Ubuntu 18.

Binaries include:

  • Mac version - includes boost, readline, gsl, hdf5
  • Windows - includes boost
  • Ubuntu - includes boost, readline (version 7), gsl
  • Linux - includes boost, readline (version 6), hdf5
Assets 7

@mothur-westcott mothur-westcott released this Jun 19, 2019 · 114 commits to master since this release

  • Fixes bug in count table removeGroups functions #626
  • Fixes definitions #633
Assets 6

@mothur-westcott mothur-westcott released this May 13, 2019 · 121 commits to master since this release

  • Updates vsearch version to resolve Windows output format bug.
  • Improves removeOTU functions to increase processing speed.
Assets 6

@mothur-westcott mothur-westcott released this Apr 29, 2019 · 178 commits to master since this release

Enhancements:

  • Sets random seed to 19760620 at start of mothur. #600
  • Adds constaxonomy file to list.otus command. #581
  • Adds rename option to the get.oturep command. #555
  • Adds ability to comment out lines in the file file. #560
  • Adds merge.otus command. #558
  • Adds processors option to rarefaction.single and rarefaction.shared. #544
  • Expands make.shared to allow for count files with no groups. #563
  • Adds fastq to split.groups command. #499
  • Adds Oligos class and split.groups commands fastq.info. #499
  • Merge.count command ignores duplicate names. #259
  • Removes catchall dependency. #164
  • Improves help command. #183
  • Adds tree parameter to sub.sample command.
  • Adds withreplacement parameter to sub.sample command. #262
  • Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262
  • Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583
  • Adds taxonomy parameter to rename.seqs.
  • Removes multiple inputs from mothur. #379
  • Reduces memory needed for pre.cluster #589
  • Adds count parameter to count.seqs to inflate or deflate count tables.
  • Updates vsearch version to 2.11.1 #585
  • Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586
  • Adds constaxonomy file to subsample command. #582

Bug Fixes:

  • Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true.
  • Fixes file extensions of output files in pcr.seqs.
  • Fixes sub.sample with multiple labels bug. #559
  • Fixes bug with otu.association metadata file.
  • Fixes pcr.seqs end issue with keepdots=f.
  • Fixes bug in remove.lineage with cons.taxonomy and shared files. #580
  • Removes extra space from output. #603
  • Fixes output filename for make.group. #602
Assets 5
Pre-release

@mothur-westcott mothur-westcott released this Apr 2, 2019

Enhancements:

  • Adds rename option to the get.oturep command. #555
  • Adds ability to comment out lines in the file file. #560
  • Adds merge.otus command. #558
  • Adds processors option to rarefaction.single and rarefaction.shared. #544
  • Expands make.shared to allow for count files with no groups. #563
  • Adds fastq to split.groups command. #499
  • Adds Oligos class and split.groups commands fastq.info. #499
  • Merge.count command ignores duplicate names. #259
  • Removes catchall dependency. #164
  • Improves help command. #183
  • Adds tree parameter to sub.sample command.
  • Adds withreplacement parameter to sub.sample command. #262
  • Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262
  • Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583
  • Adds taxonomy parameter to rename.seqs.
  • Removes multiple inputs from mothur. #379
  • Reduces memory needed for pre.cluster #589
  • Adds count parameter to count.seqs to inflate or deflate count tables.
  • Updates vsearch version to 2.11.1 #585
  • Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586
  • Adds constaxonomy file to subsample command. #582

Bug Fixes:

  • Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true.
  • Fixes file extensions of output files in pcr.seqs.
  • Fixes sub.sample with multiple labels bug. #559
  • Fixes bug with otu.association metadata file.
  • Fixes pcr.seqs end issue with keepdots=f.
  • Fixes bug in remove.lineage with cons.taxonomy and shared files. #580
Assets 5
Mar 6, 2019
Updates makefile for 1.42.0 prerelease

@mothur-westcott mothur-westcott released this Jan 30, 2019 · 262 commits to master since this release

Enhancements

  • Adds timing to pre.cluster deconvolute steps.

Bug Fixes

  • classify.seqs and filter.seqs command may eliminate reads causing file mismatches.
  • get.oturep bug with abundance method.
Assets 5

@mothur-westcott mothur-westcott released this Jan 23, 2019 · 275 commits to master since this release

  • Updated on 1.23.19 to include get.oturep fix

Enhancements:

  • Adds rename option to the get.oturep command. #555
  • Adds ability to comment out lines in the file file. #560
  • Adds merge.otus command. #558
  • Adds processors option to rarefaction.single and rarefaction.shared. #544
  • Expands make.shared to allow for count files with no groups. #563
  • Adds fastq to split.groups command. #499
  • Adds Oligos class and split.groups commands fastq.info. #499
  • Merge.count command ignores duplicate names. #259
  • Removes catchall dependency. #164
  • Improves help command. #183

Bug Fixes:

  • Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared.
  • Fixes file extensions of output files in pcr.seqs.
  • Fixes sub.sample with multiple labels bug. #559
  • Fixes bug with otu.association metadata file.
  • Fixes pcr.seqs end issue with keepdots=f.
  • Fixes get.oturep crash with abundance method. #575
Assets 5
Jan 22, 2019
Moves replaces file file for git conflict
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