Sarah Westcott [Mon, 30 Jul 2012 19:25:39 +0000 (15:25 -0400)]
fixed subsample name file name issue. added count parameter to cluster command. added read to readColumn and readMatrix that uses a count table. added functions to countTable class to work with clusters reads.
Sarah Westcott [Fri, 27 Jul 2012 13:42:37 +0000 (09:42 -0400)]
added sparseDistanceMatrix class. Modified cluster commands to use the new sparse distance matrix class. cut cluster time by 55% and reduced memory usage by 50%.
Sarah Westcott [Thu, 28 Jun 2012 13:37:34 +0000 (09:37 -0400)]
added countable class to read and store count file. added count parameter to make.shared command and modified sharedlistvector to use it. fixed formatting issue related to make.shared with a biom file.
Sarah Westcott [Tue, 26 Jun 2012 15:25:18 +0000 (11:25 -0400)]
made make.table alias to count.seqs command. added large parameter to count.seqs to allow for creating the table without storing files in ram. added subsampling to rarefaction.shared. added countable current type.
Sarah Westcott [Tue, 12 Jun 2012 15:27:51 +0000 (11:27 -0400)]
changed reading of name file to use buffered reads. note the splitAtWhiteSpace function is sensitive to the gobble function. do not use the two together while reading or the read can get off track. modified trim.seqs group counts to include the redundant sees if a names file is provided. changed group maps read of a group file to be buffered. modified appendFiles functions to be buffered.
Sarah Westcott [Mon, 11 Jun 2012 16:13:55 +0000 (12:13 -0400)]
fixed bug with dist.shared subsampling. added mode parameter to dist.shared so you can select average or median for the results. added some debug code as I sorted out some bug reports to mothur.bugs.
Sarah Westcott [Mon, 4 Jun 2012 19:40:50 +0000 (15:40 -0400)]
fixed classify.seqs output file name - had issue if reference taxonomy file did not have 3 parts to the name. modified rarefaction.shared to output a group.rarefaction file when design file is used.
Sarah Westcott [Mon, 4 Jun 2012 16:27:23 +0000 (12:27 -0400)]
added check to make sure shhh.flows child processes finish properly. added subsampling to summary.shared and summary.single. modified dist.shared to run original dataset as well as subsamples when subsample=t
Sarah Westcott [Thu, 24 May 2012 16:50:47 +0000 (12:50 -0400)]
fixed bug in sffinfo when ~ was used in the sff filename. fixed issue in shhh.flows, it was producing an output file called *.flow.fasta instead of *.fasta. Also when using outputdir with the file option, it put the shhh.fasta and shhh.names files in the wrong folder. changed format of rarefaction.single output with groups to look more like the phylo.diversity command.
Sarah Westcott [Fri, 18 May 2012 16:35:51 +0000 (12:35 -0400)]
added check to cluster.classic to make sure file type is phylip. added mapping function to alignments traceback function so we can relate the position in the unaligned sequence to the aligned sequence. worked on make.contigs command
Sarah Westcott [Tue, 15 May 2012 17:54:41 +0000 (13:54 -0400)]
added list.labels command. started work on make.contigs command. fixed fastq.info and make.fastq quality scores control character. fixed bug in classify.otu that made bootstrap values for "unknown" taxon too high
John Westcott [Wed, 9 May 2012 15:31:46 +0000 (11:31 -0400)]
added debug flag to mothurOut. added debug parameter to set.dir. added debug code to catchall and get.seqs commands. created newcommandtemplate. started work on get.coremicrobiom command. fixed command parameter bug in chimera.bellerophon command.
Sarah Westcott [Wed, 2 May 2012 19:22:40 +0000 (15:22 -0400)]
fixed segfault in unifrac with subsample. in progress of implementing a version of the subsample tree that sets sees you don't want to includes groups to doNotIncludeMe. to test which is more efficient.
projects / mothur.git / log