To do

Reference sequences

• Add B cell receptors.

• Add a make target to refresh the reference sequences from RefSeq.

• Support multiple organisms.

• Define a versionned CDR3 file format and test it before reading in read clonotypes.R

read_clonotypes: do not hardcode column classe, but infer them from the name, that is inferred from the OSC header, or hardcoded as a fallback.

OSCTable support

Define

##ProtocolREF = CP-Custom-v1.0

Correct in OSC file

##ParameterValue[qual] = Illumina

Is it correct to have same name for ParameterValue and ColumnName ?

Do we need ?

##NameSpace = genomic_coordinate

• Provide example AB1 and SFF files.

Others

Get good default for CLONOTYPER_REFERENCE and other variables.

Regression tests: make sure that the example data has a sharp sign in the FASTQ sequence (if valid), and compare the number of lines to what is expected.

Support extraction of barcoded reads.

Report the number of V segments found after clonotypeR detect.

Clonotype algebra, like in:

`+.clonotypeList` <- function(X, Y) structure( union(X, Y),     class='clonotypeList')
`^.clonotypeList` <- function(X, Y) structure( intersect(X, Y), class='clonotypeList')
`-.clonotypeList` <- function(X, Y) structure( setdiff(X, Y),   class='clonotypeList')