ufits v0.4.0

• improvement to ufits filter script to handle some of the filtering more gracefully and added a few more options
• added ability to supply a list of samples/barcodes to ufits remove and ufits select to make more flexible
• add new clustering module based on reference based clustering called ufits cluster_ref, it functions by quality trimming, dereplicating, chimera filtering, mapping to reference database. It can then also rescue unmapped reads and run de novo clustering on them followed by UTAX reference based clustering. I think that standard de novo clustering is superior to this approach but in some fringe cases it may be useful.

ufits v0.3.16

• slight modification to ufits show that also shows read lengths
• minor bug fix in ufits taxonomy that now properly exits if databases not installed
• changed the way ufits filter calculates index bleed from a sum of all counts per OTU, to now using the maximum value per sample.
• upgrade to ufits meta to also allow for splitting up data by taxonomy classification (if taxonomy from UFITS default method)

ufits v0.3.14

• added ufits show to count barcodes from demuxed data
• fixed bug in ufits filter if try to use -s auto option without providing a --mock_barcode

ufits v0.3.13

• bug fix where clustering log file was getting overwritten

ufits v0.3.12

• bug fix to ufits filter where the --col_order option now checks for samples before sorting to avoid error if sample passed but not in dataset, now it is ignored
• bug fix to ufits filter if using -s and --keep_mock options - script would die

ufits v0.3.11

• minor update to annotate mock community mapping to OTUs in ufits filter

ufits v0.3.10

• bug fix where ufits filter did not rename fasta headers for OTUs that were mapped from the mock community
• changed filename of output OTUs from ufits cluster to basename.cluster.otus.fa

ufits v0.3.8

• added a check for vsearch version, need > v1.9.1

ufits v0.3.7

• updates to support looking at full length amplicons instead of trimming and padding. Only recommended to use if you know what you are doing

ufits v0.3.6

• minor fix of ufits cluster using vsearch where if read length --length was longer than actual length of reads then vsearch crashes. Now scripts calculate read length and adjust appropriately
• added some output to stdout for filter command to let users know where files are located