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@mothur-westcott mothur-westcott released this Nov 9, 2018 · 290 commits to master since this release

  • Add sample info to tax.summary in biom.info command. #531
  • Updates biom.info to read hdf5 biom files. #178
  • make.contigs change to quality score calculation. #468
  • Adds oldfasta and column parameters to pairwise.seqs command.
  • Adds testing features
  • Adds count file to shared file option in make.shared command. #519
  • Updates boost version to 1.68.0.
  • Adds fasta, taxonomy, name and count options to merge.files. #506
  • Updates get.oturep command to use optiMatrix. Reduces time and memory needed. #465
  • Prevent excessive log file size by limiting errors and warnings for commands to 10. #420
  • Adds relabund to create.database command. #478
  • Adds multiple cutoffs to cluster command for opti, agc and dgc. #305
  • Adds accnos parameter to filter.shared. #293
  • Adds shared and groups parameters to get.rabund command. #325
  • Adds unoise, tree, deblur methods to pre.cluster command.

Bugs

  • unifrac command crashes with subsample option.
  • cluster command nearest neighbor bug fix
  • collect.shared "[ERROR]: requesting groups not present in files, aborting." error #497
  • Removes extra "quit()" output. #464
  • Fixes make.contigs group file issue with *.gz files. #480
  • Fixes pcr.seqs file mismatch. #522
  • Tree.shared command results with shared file. #535
  • Make.contigs group names. https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542
  • Fixed 1.40.1 - Mothur's logfile created in mothur's executable location, instead of current working directory. #436
  • Fixed 1.40.1 - Smart distancing hangs if label not found in file. #441
  • Fixed 1.40.2 - Fixes *contigs.report file append issue that resulted in reads missing from report.
  • Fixed 1.40.3 - get.coremicrobiome command segfault with shared option. #445
  • Fixed 1.40.3 - merge.files not finding input files. #438
  • Fixed 1.40.3 - sparcc improves speed with threaded code and corrects small bug.
  • Fixed 1.40.4 - Cluster commands printing of list file. #454
  • Fixed 1.40.4 - Cluster.split merge of list files bug #460
  • Fixed 1.40.4 - Cluster commands - method agc and dgc do not require distance matrix. #456
  • Fixed 1.40.4 - Trim.seqs multiple matches error. #427
  • Fixed 1.40.4 - Pre.cluster name / group error. #461
  • Fixed 1.40.4 - Pre.cluster single sample crash. #451
  • Fixed 1.40.4 - pcr.seqs and screen.seqs (with no bad reads detected), causing accnos file issue.
  • Fixed 1.40.5 - get.lineage failing to find taxons. #477
  • Fixed 1.40.5 - screen.seqs not making *good.groups or *good.count_table files. #476
  • Fixed 1.40.5 - get.communitytype crash. #472
  • Fixed 1.40.5 - Fixes make.contigs gz file read issues. #471
  • Fixed 1.40.5 - Solves seq.error crash #463
  • Fixed 1.40.5 - Resolves trim.seqs "could not open" error. #444
Assets 5
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