0.7.0 (in progress)

Fix for kallisto output failing due to defaultdict not being imported. Thanks to @andreas-wilm for the fix.
Added tagcount option --parse_tags to use BAM tags rather than parsing read names (UM for UMI, CR for cell barcode)
Added tagcount option --gene_tags to use BAM tags to get ID of mapping gene (GX tag).

0.6.0

Fix skipping first piece of evidence when tagcounting.
Add test for tagcount.
Output full sorted transcript table from tagcount rather than only the observed transcripts.
Add --sparse option to output tagcount matrices in MatrixMarket format.
Allow cb_histogram subcommand to take gzipped files.
Allow cb_filter subcommand to take gzipped files.
Add support for triple-cellular barcodes.
Add example for Illumina SureCell (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/surecell-wta-ddseq.html)

Fix automatic format detection in cb_histogram.
Add tests for cb_histogram.
Re-enable streaming bamtagging. Thanks to @chapmanb for the suggestion.
Add subset_bamfile to subset a BAM file to keep alignments with a given set of cellular barcodes.
Speed improvements for reading gzipped FASTQ files.
Memory usage improvements for tagcount.

Fix for handling unicode, thanks to @chapmanb and @sowmyaiyer
Adds support for adding BAM tags to aligned fastqtransformed files. Thanks to @chapmanb.
Adds support for UMI-only fastqtransformation.
Adds support for paired-end target sequences.
Adds support for detecting sample barcodes via the SB tag in the regex.
Adds support for sample-based demultiplexing with error correction.

Now supports transforming 3-file input, as from the Linnarsson lab STRT-Seq data
New kallisto subcommand formats read files for input to kallisto's UMI mode
Fix gzip based fastq reading on Python 3.5
Including preliminary subcommand for guessing cell cutoff from cb_histogram