ChangeLog

Version 2.32:
- Added a program to merge overlapping paired end Illumina reads
- Fixed bug: removed hard limit on seqeunce lengeth (was 500nt).





Version 2.31:
- Fixed bug: structure to hold parameters was not passed correctly to the main when no parameters were used...

Version 2.3:
- Added basic error handling.
- Fixed bug where fingerprint was not reported in the output.

Version 2.2:
- Added support for demultiplexing Illumina 1.8.4 files (Instead of illumina default).
- Tagdust can now be used on an arbitrary number of input files provided that only one (none) contains a barcode.

Version 2.12:
- Fixed help output. 

Version 2.06:
- TagDust now supports extracting multiple reads from single input sequences. 
- fixed bug prining out two '@' signs for read names. 
- fixed bug only partially printinting out sequence names. 

Version 2.05:
- added useability options. 
- fixed some minor bugs.

Version 2.04:
- new random model: If the reads are expected to include barcodes, I simply add another N{x} barcode. Reads which do not have the barode will use this HMM.   


Version 2.03:
- Several bugfixes:
        - crashed when linkers were longer than 32 nucleotides. 
        - nuc_code array was set to length 255 not 256 

Version 2.01:

- added simple read filtering by matching to a reference, 
- added better support for partial segments ( 5' and 3' adapters)
- more input checking...