Initial empty master branch.
Added reference TCR genes from RefSeq, but BCRs and update helper are needed.
Extraction of the V, (D), J and C segments from the reference sequences.
Reference V and J alignment (made by hand using SeaView).
Reference V and J segments trimmed at C or FGxG motifs.

Needed for V-J extraction by the “VJsplit” script.
BWA index of trimmed V segments.
Function “read.clonotypes” to load a clonotypes file, and example data.
Integrate the calculation of the eight column: improductive rearrangements.
Test data using three libraries.
New function to prepare clonotype tables.
A function to list unique clonotypes.
Reordered options in clonotype.table, and corrected for single libraries.
Standardised options, shortened error messages, added one check.
Draft instructions and script to extract clonotypes.
Preparing the use of the OSCTable format.
Added codon ID table for the Yassai nomenclature.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706371/table/Tab1/
First step to implement Yassai's nomenclature: the CDR3.
Replace NA per FALSE; is.somatic is used in a while loop.
Attempt at pre-loading J_before_FGxG and V_after_C.

This will probably not work du permier coup.
Documented what the code is doing.