It's Christmas

• Configuration syntax changes to accommodate new features. Please review the documentation and examples.
• Support for a single Sample decoder and multiple cellular and molecular decoders.
• Support for output splitting by any of the decoders (but only one) explicitly by using the multiplexing classifier tag or implicitly by declaring output in a decoder.

The new world

• Fix for a help printing bug #17
• speed improvement and a new attempt to control thread allocation automatically
• fix a bug that prevented compiling a job without a configuration file in some cases
• a much improved optimized Shannon bound search that consumes much less memory when the barcode set is HUGE

Now in Technicolor

Tested with zlib 1.2.11, bzip2 1.0.6, xz 5.2.4, libdeflate 1.0, htslib 1.9, rapidjson 1.1.0.

Fixed:
Fix decoding from SAM with 4 byte padded qname

Changed

• demux sub command renamed mux

Added:

• Support for multiplex, molecular and cellular barcode SAM aux tags.
• Tree Inheritance between decoder definitions in the decoder tag.
• Importing external configuration files with the import tag.
• More precise tests for SAM output and reports.
• Support for routing the JSON report to a specific file instead of stderr

Not yet implemented:

• Support for concatenating multiple inputs into output
• Support for transcoding auxiliary tags and alignment related SAM fields
• Support for output definitions on molecular or cellular decoders

1.0

I’ll build my own theme park

• Builds against HTSlib 1.4 and RapidJSON 1.1.0
• Experimental support for linting a config file made it in time, but the canonical syntax might change slightly in the future.
• Supports the new Thread pool model in HTSlib 1.4
• Input file format sensing
• Support for shell variables in paths