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.
removed initmatrix and replaced it with co_matrix. With the re-written command there shouldn't be a need to keep the initial matrix, it's just taking up memory.
Sarah Westcott [Wed, 11 Apr 2012 15:35:07 +0000 (11:35 -0400)]
fixed bug with windows version of trim.seqs when run with 1 processor. fixed file output redirect for shhh.slows command. modified mothur so that you can set input and output directories using the parameters in the command.
Sarah Westcott [Thu, 5 Apr 2012 13:52:08 +0000 (09:52 -0400)]
added subsample, tiers and processors to tree.shared command. removed bootstrap.shared command. converted consensus command to a class. fixed a few small things related to binLabels.
Sarah Westcott [Mon, 2 Apr 2012 14:14:38 +0000 (10:14 -0400)]
added create.database command. fixed help in get.sharedseqs. added new constructor to sequence class to get comment strings after sequence name. fixed filenames in sffinfo when sff file did not end in .sff. removed debugging c out statement from trim.flows.
Sarah Westcott [Tue, 27 Mar 2012 16:35:08 +0000 (12:35 -0400)]
added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error if group names contained '_' in shared file. metastats - modified to more closely follow results from metastats website. trim.flows and trim.seqs allow for characters other than ATGC in reverse primers. removed name file warning when mother calls command internally.
Sarah Westcott [Tue, 6 Mar 2012 12:54:36 +0000 (07:54 -0500)]
changed sffinfo flow default to true. fixed bug in trim.seqs and filter.seqs related to windows paralellization mods, added help and description to concurrence command
Sarah Westcott [Mon, 5 Mar 2012 14:59:50 +0000 (09:59 -0500)]
fixed classify.seq error message when flip accnos file was blank. Fixed bug with phylotype command related to the addition of "unknown" classification in phylotree.