mothur/mothur

Forces abort for Windows vsearch method

Adds 1.37 to master branch

Clears testing vectors …

Avoids bad_allocs due to push_back error

Trying to get back to a good state

Adds unit tests for vsearchParser class

Fixed bug with class count …

Lefse command, Skipping iters warning

Adds vsearchfileparser and average linkage to testProject …

Resolves pesky linking issue

WIP Testing Updates

Creates dataset class for testing …

Includes data from final.fasta, final.names, final.groups, final.count_table and final.an.shared.

Adds fastqread to remove.seqs …

#113

Adds fastqread to parse.fastq command …

#113

Adds fastqread class to make.fastq command …

#113

Adds fastq class to list.seqs …

#113

Adds fastqread class to get.seqs …

#113

Adds count parameter to get.sharedseqs …

#133

Adds parent taxon to unclassifieds. …

Classify.seqs, classify.otu, biom.info

#29

Adds parent taxon to unclassifieds in classify.seqs …

#29

Adds threshold parameter to summary.tax …

#31

Adds printlevel to classify.seqs, classify.otu, biom.info and summary… …

….tax

#158

Adds relabund parameter to classify.otu …

#101

Merge pull request #217 from mothur/Issue204_ClassifyOutput …

Adds output parameter to *tax.summary file

Adds output parameter to *tax.summary file …

#204

mothur-westcott committed Mar 15, 2016

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Merge remote-tracking branch 'origin/v.1.37.0' into v.1.37.0

Fixing Travis build

Merge pull request #214 from mothur/Issue167 …

Issue167

Merge branch 'Issue167' into v.1.37.0

Adds namecheck changes to windows code …

#167

mothur-westcott committed Mar 14, 2016

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Sets nameType at file setup to save processing time …

Fixes name mismatch bug #167

mothur-westcott committed Mar 14, 2016

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Updates external makefile

Fixes cluster.split bug with sequences not assigned to group …

When I added the changes for the vsearch methods I added checks to make sure there were no singletons in that splitting case.  The sequences mothur is complaining about have a tax level below the cutoff, and so they are not assigned to a group and should be singletons.   I remembered the below the distance cutoff  but forgot about the below the taxlevel cutoff.

Adds includescrap parameter to make.sra …

#109

Replaces load.logfile with updates to set and get.current …

#110

Fixes windows bug where processors adjust was set+1 …

If number of processors was greater than number of sequences than we meant to adjust processors to number of sequences, but instead were adjusting to the number of file positions.  The number of file positions is the number of sequences + 1.  Rare bug caused empty file error.

#195

Fixes summary.seqs output to remove -1's

Changes minlength=10 in screen.seqs …

#160